Contacts of the helix formed by residues 153 - 175 (chain A) in PDB entry 3RKR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A TRP* 3.9 8.3 - - - -
96A PHE* 3.8 21.1 - - - -
150A VAL* 3.0 14.6 + - - +
151A ALA 3.1 1.8 + - - -
152A ASP* 1.3 78.9 - - - +
154A ALA* 1.3 58.1 + - - +
155A ALA 3.5 2.5 - - - -
156A TYR* 3.3 4.4 + - - +
157A THR* 2.8 34.7 + - - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TRP* 6.0 1.8 - - - -
100A LEU* 3.9 38.3 - - + +
150A VAL 3.6 5.8 + - - +
152A ASP 3.7 4.1 - - - +
153A GLY* 1.3 77.4 - - - +
155A ALA* 1.4 58.3 + - - +
157A THR* 3.3 7.0 + - - -
158A ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TRP* 5.9 1.7 - - + +
100A LEU* 4.4 4.0 - - + +
103A MET* 3.4 39.7 - - + -
108A TRP* 3.7 28.9 - - + -
111A LEU* 3.6 11.3 - - + +
112A ILE* 4.4 2.4 - - + +
154A ALA* 1.4 74.3 - - - +
156A TYR* 1.3 67.5 + - - +
158A ALA* 3.2 5.3 + - - +
159A SER* 2.9 23.7 + - - -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL 3.5 27.4 - - - -
94A GLY* 3.9 6.1 - - - -
95A TRP 4.4 3.7 + - - +
96A PHE* 3.7 37.5 - + + -
111A LEU* 3.9 12.9 - - + +
115A ASN* 4.0 4.3 - - - -
143A SER* 2.4 31.8 + - - -
144A LEU* 3.9 27.1 - - + -
150A VAL* 5.1 3.6 - - + -
153A GLY* 3.4 14.1 - - - +
155A ALA* 1.3 79.6 - - - +
157A THR* 1.3 63.3 + - - +
159A SER* 2.7 24.3 + - - -
160A LYS* 3.1 25.8 + - + +
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.7 12.1 - - + -
149A PRO* 4.0 18.2 - - + -
150A VAL* 3.2 26.6 + - - +
153A GLY 2.8 23.9 + - - -
154A ALA* 3.5 7.0 - - - -
156A TYR* 1.3 70.1 - - - +
158A ALA* 1.3 66.0 + - - +
159A SER 3.2 0.3 + - - -
160A LYS* 3.2 1.9 + - - -
161A TRP* 3.0 56.1 + - + +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TRP* 4.9 14.4 - - + -
112A ILE* 5.2 3.8 - - + -
116A LEU* 5.1 2.4 - - - +
154A ALA 2.9 17.7 + - - +
155A ALA* 3.2 12.8 + - - +
157A THR* 1.3 72.5 - - - +
159A SER* 1.3 57.2 + - - +
161A TRP* 4.3 3.9 - - - +
162A GLY* 2.9 28.1 + - - -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.6 9.3 - - - +
112A ILE* 4.0 14.1 - - - +
115A ASN* 3.1 42.4 + - - +
116A LEU* 3.9 12.7 - - - +
155A ALA 2.9 12.5 + - - -
156A TYR 2.7 18.8 + - - -
158A ALA* 1.3 78.4 - - - +
160A LYS* 1.3 59.7 + - - +
162A GLY 3.7 0.7 - - - -
163A LEU* 2.8 28.1 + - - +
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 5.4 1.0 + - - -
92A GLY* 4.5 11.9 - - - -
115A ASN* 3.7 38.0 + - + +
141A ILE 4.9 7.3 + - - -
142A SER* 4.0 11.0 - - - +
143A SER* 3.8 35.9 + - - +
144A LEU* 3.9 23.3 - - + -
156A TYR* 3.1 30.1 + - + +
157A THR 3.2 4.0 + - - +
159A SER* 1.3 76.8 - - - +
161A TRP* 1.3 65.5 + - - +
162A GLY 3.2 0.9 - - - -
163A LEU* 3.2 12.8 + - + +
164A ASN* 2.9 31.0 + - - +
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Residues in contact with TRP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.5 11.2 - - + +
146A GLY* 3.4 45.0 - - - +
147A LYS 3.5 28.6 - - - +
148A ASN 3.9 15.7 + - - -
149A PRO* 4.0 9.4 - - + -
157A THR* 3.0 40.8 + - + +
158A ALA* 4.3 4.0 - - - +
160A LYS* 1.3 76.2 - - - +
162A GLY* 1.3 62.8 + - - +
164A ASN* 3.4 10.7 + - - +
165A GLY* 3.1 18.7 + - - -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.5 16.7 - - - +
158A ALA 2.9 19.7 + - - -
159A SER 3.8 0.9 - - - -
161A TRP* 1.3 77.8 - - - +
163A LEU* 1.3 56.1 + - - +
165A GLY* 3.1 2.4 + - - -
166A LEU* 2.9 30.3 + - - +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 5.7 1.8 - - + +
115A ASN 4.1 9.4 - - - +
116A LEU* 3.5 7.1 - - + +
119A PRO* 3.8 35.2 - - + -
140A ASN* 4.4 16.2 - - + +
141A ILE 4.1 12.3 - - - +
142A SER* 4.1 26.2 - - - +
159A SER 2.8 19.5 + - - +
160A LYS* 3.2 14.3 + - + +
162A GLY* 1.3 72.2 - - - +
164A ASN* 1.3 61.7 + - - +
166A LEU* 3.2 8.8 + - + +
167A MET* 2.9 46.8 + - + +
183A LEU* 4.9 1.6 - - + -
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 2.9 21.0 + - - -
144A LEU 3.2 22.0 + - - -
145A ALA* 3.7 6.7 + - - +
146A GLY* 3.6 20.6 - - - +
160A LYS 2.9 10.5 + - - -
161A TRP* 3.5 9.2 - - - +
163A LEU* 1.3 75.5 - - - +
165A GLY* 1.3 54.6 + - - +
167A MET* 4.1 0.2 - - - -
168A THR* 2.8 38.8 + - - +
183A LEU* 3.4 31.5 - - + +
185A ALA* 5.8 1.1 - - - +
230A GLU* 5.7 2.5 + - - -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TRP 3.1 14.8 + - - -
162A GLY* 3.1 2.7 + - - -
164A ASN* 1.3 72.5 - - - +
166A LEU* 1.3 62.1 + - - +
168A THR* 4.0 5.2 - - - -
169A SER* 2.8 34.1 + - - -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.0 23.1 - - + +
120A TYR* 3.9 29.6 - - + +
162A GLY 2.9 16.9 + - - +
163A LEU* 3.3 10.1 - - + +
165A GLY* 1.3 77.2 - - - +
167A MET* 1.3 83.8 + - + +
169A SER* 3.4 5.4 + - - -
170A ALA* 3.0 26.7 + - + +
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 4.0 4.0 - - - +
119A PRO* 3.5 38.8 - - + +
120A TYR* 4.7 0.2 - - - -
123A LEU* 3.8 24.5 - - + -
138A ILE* 4.7 1.1 - - + -
140A ASN* 3.3 44.4 - - + +
163A LEU* 2.9 27.5 + - + +
164A ASN 4.4 0.9 - - - +
166A LEU* 1.3 85.9 - - + +
168A THR* 1.3 61.0 + - - +
170A ALA* 3.3 2.2 + - - +
171A ALA* 2.9 30.3 + - - +
181A VAL* 3.6 20.2 - - + +
183A LEU* 4.8 11.7 - - + -
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 2.8 24.0 + - - +
165A GLY* 4.0 5.8 - - - -
167A MET* 1.3 78.3 - - - +
169A SER* 1.3 62.2 + - - +
171A ALA* 3.5 11.3 + - - +
172A GLU* 3.7 21.2 + - - +
183A LEU* 4.1 13.9 - - - +
230A GLU* 5.7 0.2 + - - -
187D GLY 5.4 2.7 - - - +
234D ARG* 4.0 15.8 + - - +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLY 2.8 23.5 + - - -
166A LEU* 3.6 5.6 - - - -
168A THR* 1.3 76.4 - - - +
170A ALA* 1.3 64.3 + - - +
172A GLU* 3.1 19.4 + - - +
173A GLU* 3.3 24.2 + - - +
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.8 30.7 - - + -
166A LEU* 3.0 18.1 + - + +
167A MET* 3.3 8.3 + - - +
169A SER* 1.3 77.1 - - - +
171A ALA* 1.3 62.0 + - - +
173A GLU* 3.1 20.7 + - - +
174A LEU* 3.0 29.5 + - + +
181A VAL* 4.1 4.5 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET 2.9 17.0 + - - +
168A THR* 3.7 7.9 - - - +
169A SER 3.1 0.2 - - - -
170A ALA* 1.3 76.5 - - - +
172A GLU* 1.3 60.8 + - - +
174A LEU* 4.6 0.2 - - - +
175A ARG* 3.3 28.2 + - - +
179A VAL 5.1 0.4 - - - +
181A VAL* 3.9 31.8 - - + +
227A PHE* 4.2 13.3 - - + -
229A SER* 5.7 0.7 - - - -
234D ARG* 4.0 18.2 - - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 3.7 15.9 + - - +
169A SER* 3.1 11.7 + - - +
171A ALA* 1.3 76.6 - - - +
173A GLU* 1.3 62.1 + - + +
175A ARG* 3.8 13.7 - - - +
176A GLN* 4.7 5.2 + - - -
241A SO4 3.4 17.8 + - - +
188D SER* 4.5 7.1 - - - -
189D VAL* 5.5 5.5 + - - +
234D ARG* 2.7 32.1 + - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 6.1 1.0 - - - +
169A SER* 3.4 22.3 - - - +
170A ALA* 3.1 20.3 + - - +
172A GLU* 1.3 79.7 - - + +
174A LEU* 1.3 68.8 + - + +
176A GLN* 3.4 27.1 + - - +
177A HIS* 4.2 4.3 - - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.2 15.5 - - + -
127A ALA* 4.4 10.8 - - + -
131A ILE* 3.7 36.1 - - + -
138A ILE* 4.1 19.3 - - + -
170A ALA* 3.0 17.3 + - + +
173A GLU* 1.3 82.2 - - + +
175A ARG* 1.3 57.2 + - - +
176A GLN 3.1 3.4 - - - -
177A HIS* 2.8 32.1 + - + +
179A VAL* 3.3 33.9 + - + +
181A VAL* 3.7 24.5 - - + -
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA 3.3 14.4 + - - +
172A GLU 3.8 13.0 - - - +
174A LEU* 1.3 77.8 - - - +
176A GLN* 1.3 63.6 + - + +
178A GLN* 2.9 23.6 + - - -
179A VAL 3.5 10.5 + - - -
227A PHE* 3.9 25.0 - - + -
241A SO4 3.1 46.0 + - - -
190D ARG* 5.0 7.2 - - - +
235D PRO* 2.3 48.6 + - - +
236D THR 3.9 10.5 + - - -
237D LEU* 3.8 20.5 - - + +
238D LYS* 5.4 6.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il