Contacts of the helix formed by residues 160 - 178 (chain A) in PDB entry 4A9H
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 ASP 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASN* 3.5 10.6 - - - +
157A LYS* 2.8 55.3 + - - +
158A PRO 4.3 0.9 - - - +
159A THR* 1.3 82.2 + - - +
161A ASP* 1.3 64.2 + - - +
162A ILE* 3.9 19.1 - - + +
163A VAL* 3.2 17.7 + - - +
164A LEU* 3.9 3.1 + - - +
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Residues in contact with ASP 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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159A THR 4.4 4.7 - - - +
160A ASP* 1.3 69.7 - - - +
162A ILE* 1.3 66.3 + - - +
164A LEU* 3.0 26.1 + - + +
165A MET* 3.0 22.7 + - + +
1188A EDO 3.7 14.7 + - - +
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Residues in contact with ILE 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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98A PRO* 3.5 39.0 - - + -
99A PHE* 3.9 10.1 - - + -
152A CYS* 3.6 15.5 - - - -
156A ASN* 3.4 40.4 - - + +
160A ASP* 3.9 9.4 - - + +
161A ASP* 1.3 78.1 - - - +
163A VAL* 1.3 60.9 + - - +
165A MET* 3.3 8.5 + - - +
166A ALA* 2.9 27.9 + - - +
1188A EDO 3.7 19.1 + - - +
1189A TVP 3.7 26.2 - - + +
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Residues in contact with VAL 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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152A CYS* 4.4 9.9 - - - +
153A TYR* 3.8 16.8 - - + +
156A ASN* 4.1 18.4 - - + +
157A LYS 3.6 24.2 - - - +
158A PRO* 4.3 10.8 - - + +
160A ASP 3.2 9.1 + - - +
161A ASP 3.1 0.8 - - - -
162A ILE* 1.3 78.6 - - + +
164A LEU* 1.3 52.7 + - - +
166A ALA* 3.3 7.8 + - - +
167A GLN* 2.8 42.8 + - - +
154B ILE* 3.8 29.8 - - + -
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Residues in contact with LEU 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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95A PHE* 5.3 6.7 - - + -
160A ASP 3.9 2.1 + - - +
161A ASP* 3.0 20.2 + - + +
163A VAL* 1.3 78.6 - - - +
165A MET* 1.3 58.8 + - + +
167A GLN* 3.4 19.6 + - + +
168A THR* 2.8 38.4 + - - +
171A LYS* 6.3 1.3 - - - +
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Residues in contact with MET 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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95A PHE* 3.6 64.7 - - + +
97A TRP* 3.9 16.2 - - + +
98A PRO* 3.9 16.6 - - + -
99A PHE* 4.3 4.5 - - + -
161A ASP* 3.0 19.4 + - + +
162A ILE* 3.5 11.2 - - - +
164A LEU* 1.3 75.4 - - + +
166A ALA* 1.3 64.6 + - - +
168A THR* 3.3 3.5 + - - -
169A LEU* 3.1 30.1 + - - +
1188A EDO 3.9 22.7 - - - -
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Residues in contact with ALA 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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99A PHE* 3.8 21.4 - - + -
149A PHE* 3.8 15.7 - - + -
152A CYS* 3.8 12.1 - - + -
153A TYR* 3.4 21.1 - - + +
162A ILE 2.9 16.1 + - - +
163A VAL 3.6 4.9 - - - +
165A MET* 1.3 75.9 - - - +
167A GLN* 1.3 57.6 + - - +
169A LEU 3.3 1.6 + - - -
170A GLU* 2.8 31.9 + - - +
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Residues in contact with GLN 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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153A TYR* 3.4 21.5 + - + +
163A VAL* 2.8 27.4 + - - +
164A LEU* 3.5 33.8 + - + +
166A ALA* 1.3 70.7 - - - +
168A THR* 1.3 62.6 + - - +
170A GLU* 3.9 1.8 - - - +
171A LYS* 3.0 47.0 + - - +
119B GLN* 6.0 1.8 - - - +
146B ASN* 5.6 3.8 + - - +
150B THR* 4.2 8.9 - - + +
151B ASN* 5.8 1.8 + - - -
154B ILE* 4.1 17.2 - - - +
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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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93A HIS* 4.1 16.6 - - + +
95A PHE* 3.8 29.6 - - + -
164A LEU* 2.8 27.4 + - - +
165A MET 3.6 4.7 - - - -
166A ALA 3.2 0.2 - - - -
167A GLN* 1.3 77.4 - - - +
169A LEU* 1.3 61.7 + - - +
171A LYS* 3.5 12.7 + - - +
172A ILE* 3.4 23.7 + - + +
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Residues in contact with LEU 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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90A LEU* 3.4 30.0 - - + +
93A HIS* 3.5 44.4 - - + +
95A PHE* 3.7 10.5 - - + +
96A ALA* 4.0 7.4 - - - +
99A PHE* 3.5 39.7 - - + -
123A MET* 4.1 9.9 - - + -
149A PHE* 3.7 18.8 - - + -
165A MET 3.1 16.3 + - - +
168A THR* 1.3 75.7 - - - +
170A GLU* 1.3 63.3 + - - +
172A ILE* 3.2 4.3 + - - -
173A PHE* 3.0 18.4 + - - +
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Residues in contact with GLU 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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146A ASN* 3.9 17.7 - - - +
149A PHE* 3.5 42.5 - - + +
150A THR* 5.4 0.7 + - - -
153A TYR* 2.8 34.6 + - - +
166A ALA 2.8 18.2 + - - +
167A GLN* 3.9 3.1 - - - +
169A LEU* 1.3 78.1 - - - +
171A LYS* 1.3 55.9 + - - +
173A PHE* 3.1 10.3 + - + +
174A LEU* 2.9 32.5 + - + +
146B ASN* 3.0 34.1 + - - +
150B THR* 4.0 0.3 + - - -
170B GLU* 4.6 1.6 - - - +
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Residues in contact with LYS 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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164A LEU* 6.3 1.4 - - - +
167A GLN* 3.0 38.7 + - - +
168A THR* 3.8 10.7 + - - +
169A LEU 3.3 0.4 - - - -
170A GLU* 1.3 74.8 - - - +
172A ILE* 1.3 58.5 + - + +
174A LEU 3.4 0.3 + - - -
175A GLN* 2.9 34.8 + - - +
143B GLN* 3.1 38.6 + - + +
146B ASN* 5.3 7.2 - - - +
147B THR* 5.9 3.1 - - - -
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Residues in contact with ILE 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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89A ALA* 4.3 15.3 - - + +
90A LEU* 3.7 18.8 - - + -
93A HIS* 3.5 37.9 - - + +
168A THR* 3.4 15.9 + - + +
169A LEU* 3.2 8.6 + - - +
171A LYS* 1.3 74.0 - - + +
173A PHE* 1.3 66.9 - - - +
175A GLN* 3.5 15.0 + - - +
176A LYS* 3.0 47.1 + - + +
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Residues in contact with PHE 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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82A LEU* 5.0 1.8 - - + -
86A VAL* 3.8 25.3 - - + +
90A LEU* 4.2 7.1 - - + +
142A MET* 3.9 24.7 - - + -
145A PHE* 3.6 42.0 - + + -
146A ASN* 5.1 3.1 - - + -
149A PHE* 4.2 10.1 - + + -
169A LEU 3.0 11.9 + - - +
170A GLU* 3.3 26.9 - - + +
172A ILE* 1.3 78.6 - - - +
174A LEU* 1.3 69.6 + - + +
176A LYS* 3.3 2.1 + - - +
177A VAL* 2.9 53.5 + - + +
174B LEU* 4.4 20.6 - - + -
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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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170A GLU* 2.9 20.4 + - + +
171A LYS 3.8 3.4 - - - +
173A PHE* 1.3 92.5 - - + +
175A GLN* 1.3 65.7 + - - +
177A VAL* 3.2 3.9 + - + -
178A ALA* 3.0 21.1 + - - +
139B SER* 5.0 1.6 - - - -
142B MET* 3.4 34.4 - - + +
143B GLN* 3.5 21.5 - - - +
146B ASN* 3.3 42.2 - - + +
173B PHE* 4.3 20.6 - - + -
174B LEU* 4.6 7.0 - - + -
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Residues in contact with GLN 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 LYS* 2.9 27.5 + - - +
172A ILE* 3.7 19.5 - - - +
174A LEU* 1.3 76.8 - - - +
176A LYS* 1.3 68.3 + - + +
178A ALA* 3.3 14.7 - - - +
179A SER* 4.0 6.4 + - - -
139B SER* 3.4 25.6 + - - +
143B GLN* 3.5 10.2 - - - +
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Residues in contact with LYS 176 (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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81A TYR* 2.5 31.7 + - - +
85A VAL* 4.0 20.9 - - + +
86A VAL* 3.6 27.4 - - + -
89A ALA* 4.2 20.0 - - - -
172A ILE* 3.0 34.7 + - + +
173A PHE* 3.7 2.5 - - - +
175A GLN* 1.3 81.0 - - + +
177A VAL* 1.3 64.0 + - - +
179A SER* 3.0 8.8 + - - -
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Residues in contact with VAL 177 (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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81A TYR* 4.6 1.1 - - - -
82A LEU* 4.4 16.6 - - + -
86A VAL* 4.7 1.3 - - + -
142A MET* 3.9 19.7 - - + -
173A PHE* 2.9 52.2 + - + +
174A LEU* 3.2 7.2 + - + +
176A LYS* 1.3 75.6 - - - +
178A ALA* 1.3 61.9 + - - +
179A SER 3.2 1.2 + - - -
180A MET* 3.2 27.5 + - + +
142B MET* 4.0 3.8 - - + -
174B LEU* 5.4 2.7 - - + -
177B VAL* 3.5 31.2 - - + +
180B MET* 4.9 1.4 - - - +
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Residues in contact with ALA 178 (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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174A LEU 3.0 11.0 + - - +
175A GLN 3.3 15.0 - - - +
176A LYS 3.1 0.4 - - - -
177A VAL* 1.3 77.9 - - - +
179A SER* 1.3 57.6 + - - +
180A MET 3.5 1.3 - - - +
78B GLN* 3.2 27.0 + - - +
138B ALA* 5.0 2.0 - - + -
139B SER* 4.1 20.6 - - - +
142B MET* 3.8 18.1 - - - +
180B MET* 3.6 16.0 - - + +
182B GLN* 5.4 0.5 - - - +
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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