Contacts of the helix formed by residues 183 - 200 (chain A) in PDB entry 4YC3
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 THR 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A HIS* 3.6 52.2 - - + +
124A VAL 5.7 0.2 - - - +
125A LEU* 3.5 15.1 - - + +
182A SER* 1.3 87.0 + - - +
184A PRO* 1.4 72.6 - - - +
185A VAL 3.0 1.5 + - - -
186A ASP 3.1 11.0 + - - -
187A ILE* 3.5 9.3 + - - +
169B TYR* 4.7 16.6 - - + -
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Residues in contact with PRO 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 4.2 2.0 - - - +
182A SER* 3.1 16.8 - - - +
183A THR* 1.4 97.1 - - - +
185A VAL* 1.3 60.5 + - - +
187A ILE* 3.1 10.0 + - + -
188A TRP 3.0 15.2 + - - -
272A PRO* 3.4 39.3 - - + +
275A ARG* 2.9 38.8 + - + +
276A ILE 5.9 0.4 - - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.2 11.2 - - + -
127A ARG* 4.8 10.5 - - + -
160A TYR* 5.1 3.4 - - - +
171A SER* 3.3 23.6 + - - +
173A GLU* 3.1 21.3 - - - +
174A VAL* 4.0 5.6 - - + -
181A TYR* 3.7 35.0 - - + -
182A SER 3.1 19.6 + - - +
183A THR 3.0 0.4 + - - -
184A PRO* 1.3 77.3 - - - +
186A ASP* 1.3 72.9 + - - +
188A TRP* 3.5 4.3 - - - +
189A SER* 3.3 24.1 + - - -
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.7 18.4 - - + +
120A HIS* 3.0 33.8 + - + +
125A LEU* 3.4 9.8 - - - +
126A HIS* 2.9 25.6 + - - +
127A ARG* 3.0 28.3 + - - -
129A LEU* 3.9 6.8 - - + +
183A THR 3.1 3.8 + - - +
185A VAL* 1.3 77.9 - - - +
187A ILE* 1.3 59.8 + - - +
189A SER* 3.4 8.3 + - - -
190A ILE* 3.1 32.5 + - - +
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 4.8 3.8 - - + -
116A ILE* 4.2 8.7 - - + -
120A HIS* 4.3 7.2 - - + -
183A THR* 3.8 13.5 - - - +
184A PRO* 3.1 10.4 + - + +
186A ASP* 1.3 76.4 - - - +
188A TRP* 1.3 65.5 + - - +
190A ILE* 3.3 20.8 + - + +
191A GLY* 3.0 20.1 + - - -
267A MET* 4.0 31.7 - - + +
275A ARG* 4.3 6.7 - - + -
276A ILE* 3.3 28.7 - - + +
277A SER* 4.7 1.6 - - - -
278A GLY* 3.5 31.9 - - - +
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Residues in contact with TRP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TRP 5.3 0.6 + - - -
169A TYR 3.7 7.6 - - - -
170A ARG 3.2 24.4 + - - -
171A SER* 3.6 13.0 - - - -
172A PRO* 3.6 32.3 - - + -
184A PRO 3.0 11.8 + - - +
185A VAL 3.5 9.9 - - - +
187A ILE* 1.3 76.4 - - - +
189A SER* 1.3 66.0 + - - +
191A GLY* 3.0 12.0 + - - -
192A THR* 3.1 24.7 + - + +
204A PHE* 4.1 12.1 - + - -
212A GLN* 6.1 0.2 - - - +
216A ILE* 3.9 28.9 - - + +
220A LEU* 3.8 22.9 - - + -
267A MET 3.8 9.1 + - - -
268A LEU* 3.5 40.8 - - + +
269A ILE 4.2 5.6 - - - -
270A TYR* 4.5 3.8 - + - -
275A ARG* 3.8 18.8 - - - +
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG 5.3 4.7 + - - -
129A LEU* 4.0 33.2 + - - +
169A TYR* 2.6 27.1 + - - +
170A ARG* 4.8 1.9 + - - -
171A SER 5.1 0.2 + - - -
185A VAL 3.3 12.2 + - - -
186A ASP* 3.6 10.9 + - - -
187A ILE 3.3 0.2 - - - -
188A TRP* 1.3 79.8 - - - +
190A ILE* 1.3 61.5 + - - +
192A THR* 2.6 22.5 + - - -
193A ILE* 3.0 14.4 + - - +
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.6 27.1 - - + +
112A ILE* 3.7 24.5 - - + -
113A LEU* 4.1 15.5 - - + -
116A ILE* 3.7 39.9 - - + -
129A LEU* 3.8 11.4 - - + -
186A ASP 3.1 23.4 + - - +
187A ILE* 3.7 14.4 - - + +
188A TRP 3.3 0.2 - - - -
189A SER* 1.3 72.9 - - - +
191A GLY* 1.3 52.1 + - - +
193A ILE* 3.1 10.9 + - + +
194A PHE* 2.6 33.6 + - - +
267A MET* 4.2 6.7 - - + -
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Residues in contact with GLY 191 (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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187A ILE 3.0 13.4 + - - -
188A TRP 3.0 5.3 + - - -
190A ILE* 1.3 75.4 - - - +
192A THR* 1.3 60.5 + - - +
194A PHE* 3.1 1.8 + - - +
195A ALA* 3.0 19.8 + - - +
264A LEU* 3.2 20.3 - - - +
267A MET* 3.7 27.8 - - - -
268A LEU* 4.4 4.9 - - - -
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TRP 4.1 10.3 - - - +
169A TYR* 3.2 24.6 - - - -
188A TRP* 3.1 30.2 + - + +
189A SER* 2.6 24.8 + - - -
191A GLY* 1.3 73.8 - - - +
193A ILE* 1.3 60.1 + - - +
195A ALA* 3.6 3.6 + - - +
196A GLU* 3.2 22.7 + - - +
203A LEU* 4.5 19.6 + - + +
204A PHE* 3.9 27.6 - - + -
268A LEU* 4.4 4.2 - - + +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.3 14.8 - - + -
109A LEU* 6.1 0.4 - - + -
112A ILE* 4.7 7.0 - - + -
129A LEU* 4.0 11.4 - - + +
130A LYS* 3.7 34.5 - - - +
131A PRO* 4.3 6.7 - - + -
134A LEU* 4.2 25.4 - - + -
169A TYR* 3.9 17.7 - - + -
189A SER 3.0 21.1 + - - +
190A ILE* 3.5 12.6 - - + +
192A THR* 1.3 76.9 - - - +
194A PHE* 1.3 55.9 + - - +
196A GLU* 3.0 6.1 + - + +
197A LEU* 2.8 42.0 + - + +
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Residues in contact with PHE 194 (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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105A VAL* 4.0 12.3 - - + -
109A LEU* 3.5 39.9 - - + +
190A ILE 2.6 17.2 + - - +
191A GLY* 3.2 10.3 - - - +
193A ILE* 1.3 71.6 - - - +
195A ALA* 1.3 64.2 + - - +
197A LEU* 3.3 9.7 + - - +
198A ALA* 3.1 19.8 + - - +
256A LEU* 3.6 23.3 - - + -
260A GLY* 3.5 24.7 - - - -
263A LEU* 3.8 11.0 - - + -
264A LEU* 3.9 24.0 - - + -
267A MET* 4.2 6.7 - - - -
286A TYR* 3.6 32.8 - + - -
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Residues in contact with ALA 195 (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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191A GLY 3.0 12.0 + - - +
192A THR 3.7 8.7 - - - +
193A ILE 3.2 0.2 - - - -
194A PHE* 1.3 79.2 - - - +
196A GLU* 1.3 57.8 + - - +
198A ALA* 3.3 5.1 + - - +
199A THR* 2.9 36.9 + - + +
201A LYS 4.5 0.7 - - - -
203A LEU* 3.9 34.1 - - + -
253A VAL* 4.8 10.3 - - + -
256A LEU* 5.0 0.9 - - - -
264A LEU* 4.4 15.2 - - + +
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Residues in contact with GLU 196 (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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88A LYS* 5.6 3.5 - - - +
91A LEU* 4.1 18.6 - - + +
131A PRO* 3.8 15.2 - - + +
168A TRP* 5.6 1.4 - - - -
169A TYR* 2.6 37.1 + - - -
192A THR 3.2 10.4 + - - +
193A ILE* 3.0 12.4 + - + +
195A ALA* 1.3 78.2 - - - +
197A LEU* 1.3 57.8 + - - +
200A LYS* 2.7 36.5 + - - +
201A LYS 3.4 24.2 + - - +
202A PRO* 3.4 27.1 - - + +
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Residues in contact with LEU 197 (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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87A LEU* 3.8 32.3 - - + -
91A LEU* 4.2 11.4 - - + +
100A MET* 3.7 50.4 + - + +
105A VAL* 3.9 29.0 - - + +
108A TYR* 4.0 13.0 - - + -
109A LEU* 4.6 9.2 - - + +
112A ILE* 4.6 7.4 - - + -
142A ILE* 5.6 0.2 - - + -
193A ILE* 2.8 33.7 + - + +
194A PHE* 3.5 15.0 - - - +
196A GLU* 1.3 73.3 - - - +
198A ALA* 1.3 62.9 + - - +
200A LYS* 4.1 2.9 + - - +
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.8 9.4 - - - +
100A MET 5.1 1.2 + - - +
105A VAL* 4.4 12.8 - - + -
194A PHE 3.1 10.2 + - - +
195A ALA 3.6 6.7 - - - +
197A LEU* 1.3 83.7 - - - +
199A THR* 1.3 60.7 + - + +
200A LYS 3.9 0.2 + - - -
254A LYS 4.0 8.5 - - - +
255A ASN* 3.1 28.1 - - - +
256A LEU* 3.9 35.7 - - + -
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.4 19.6 - - - -
195A ALA* 2.9 19.3 + - + +
198A ALA* 1.3 72.4 - - - +
200A LYS* 1.4 65.0 + - - +
201A LYS* 2.9 48.6 + - - +
203A LEU* 6.5 0.2 - - + -
252A HIS 4.8 3.8 - - - +
253A VAL* 3.8 29.2 - - + -
254A LYS* 3.8 25.1 - - + +
255A ASN* 4.6 1.8 - - - -
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Residues in contact with LYS 200 (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 LEU* 4.0 28.2 + - + +
94A ILE* 3.1 41.1 + - + +
95A PRO 3.0 28.7 + - - -
96A PRO* 4.2 6.5 - - - +
97A GLY 4.6 1.5 - - - +
98A GLN 3.2 22.2 + - - +
99A TYR* 4.1 15.0 - - + -
100A MET 4.9 2.2 - - - +
196A GLU* 2.7 26.8 + - - +
197A LEU 4.1 1.8 + - - +
198A ALA 3.6 1.2 - - - -
199A THR* 1.4 73.2 - - - +
201A LYS* 1.3 59.8 + - + +
202A PRO* 4.5 2.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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