Contacts of the helix formed by residues 80 - 91 (chain A) in PDB entry 3AP3
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A A3P 2.8 32.9 + - - -
78A ARG 3.3 2.8 + - - -
79A SER* 1.3 71.1 - - - +
81A THR* 1.3 59.7 + - - +
82A THR 3.4 1.8 - - - -
83A LEU* 3.4 8.7 - - - +
84A MET 2.9 21.3 + - - -
181A MET* 3.6 10.7 - - - +
238A TYR* 3.8 21.3 - - - -
241A LEU* 5.2 0.2 - - - +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A A3P 2.6 20.9 + - - +
73A VAL* 4.1 1.5 - - - +
74A GLY* 3.3 34.5 - - - +
75A GLY 4.3 3.4 - - - +
76A VAL 4.4 3.8 - - - +
79A SER* 2.9 10.4 + - - +
80A GLY* 1.3 75.4 - - - +
82A THR* 1.3 60.5 + - - +
84A MET* 3.1 3.2 + - - +
85A ARG* 2.9 30.7 + - - +
158A LYS* 3.4 32.2 + - - +
160A PRO* 4.4 7.4 - - + +
181A MET* 3.5 19.3 - - + -
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Residues in contact with THR 82 (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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1A A3P 2.7 20.8 + - - -
81A THR* 1.3 72.4 + - - +
83A LEU* 1.3 67.7 + - - +
85A ARG* 3.4 25.4 + - - +
86A ALA* 2.9 26.9 + - - +
158A LYS* 3.3 21.7 + - - +
279A LEU* 4.7 6.5 - - + -
283A GLU* 4.5 10.9 + - - +
285A SER* 3.1 35.2 - - - +
286A THR* 5.4 0.2 - - - +
289A VAL* 3.9 10.8 - - + -
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Residues in contact with LEU 83 (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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1A A3P 3.5 64.3 + - + +
80A GLY* 3.4 13.6 - - - +
82A THR* 1.3 81.3 - - - +
84A MET* 1.3 64.7 + - - +
86A ALA* 3.2 9.4 + - - +
87A MET* 3.4 16.0 + - + +
238A TYR* 3.8 17.0 - - + -
241A LEU* 4.3 19.7 - - + -
242A VAL* 4.4 5.6 - - + -
267A HIS* 4.2 18.4 - - + +
289A VAL* 3.5 8.0 - - + +
293A VAL* 4.5 13.5 - - + -
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Residues in contact with MET 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.6 26.0 - - + -
80A GLY 2.9 15.4 + - - +
81A THR 3.1 8.9 + - - +
83A LEU* 1.3 77.7 - - - +
85A ARG* 1.3 62.5 + - - +
87A MET* 3.5 16.9 + - + +
88A LEU* 3.6 26.1 + - + +
179A LEU* 4.4 12.6 - - + -
181A MET* 3.7 24.9 - - + +
236A VAL* 4.3 13.7 - - - -
241A LEU* 4.5 8.7 - - - +
249A LEU* 3.9 24.2 - - + -
252A ILE* 4.3 9.0 - - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 4.3 4.0 - - + -
81A THR 2.9 14.4 + - - +
82A THR* 3.4 20.1 + - - +
84A MET* 1.3 76.0 - - - +
86A ALA* 1.3 62.4 + - - +
88A LEU* 2.9 27.6 + - - +
89A ASP* 2.9 34.4 + - - +
96A CYS* 3.8 22.4 - - + -
97A GLY 3.2 26.0 + - - -
98A GLU* 3.6 17.6 - - - +
158A LYS* 3.8 26.7 - - + +
277A VAL* 4.2 5.6 - - - +
278A SER 3.0 32.1 + - - +
279A LEU* 3.5 23.0 - - - +
280A SER 4.7 0.2 - - - +
283A GLU* 4.2 9.7 + - - -
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Residues in contact with ALA 86 (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 THR 2.9 18.9 + - - +
83A LEU 3.2 4.7 + - - +
85A ARG* 1.3 84.6 - - - +
87A MET* 1.3 60.0 + - - +
89A ASP* 3.5 1.0 + - - -
90A ALA* 3.3 6.8 + - - +
267A HIS* 3.9 11.7 - - - +
277A VAL* 3.2 44.8 - - + +
279A LEU* 5.2 0.7 - - + -
289A VAL* 3.7 25.8 - - + -
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Residues in contact with MET 87 (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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83A LEU* 3.4 22.2 + - + +
84A MET* 3.9 12.6 - - + +
85A ARG 3.2 0.6 - - - -
86A ALA* 1.3 76.9 - - - +
88A LEU* 1.3 60.8 + - - +
90A ALA* 3.8 4.1 - - - +
91A HIS 3.7 9.0 + - - -
241A LEU* 3.5 39.0 - - + -
245A PRO* 5.3 1.6 - - - -
249A LEU* 3.7 22.4 - - + -
264A VAL* 3.2 51.9 - - + +
265A LEU* 5.2 0.9 - - - -
267A HIS* 3.9 21.5 - - + +
293A VAL* 3.9 21.8 - - + -
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Residues in contact with LEU 88 (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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71A ILE* 4.5 11.7 - - + -
73A VAL* 3.9 26.0 - - + -
84A MET* 3.6 34.5 - - + +
85A ARG* 2.9 8.7 + - - +
87A MET* 1.3 78.9 - - - +
89A ASP* 1.3 63.4 + - - +
90A ALA 3.3 0.2 - - - -
91A HIS* 3.2 21.3 - - + +
94A VAL* 3.2 24.8 - - + +
96A CYS* 4.0 11.9 - - - -
156A CYS* 4.8 0.2 - - - -
179A LEU* 4.2 8.7 - - + -
249A LEU* 4.7 4.5 - - + -
252A ILE* 4.7 0.9 - - + -
253A LEU* 3.8 28.7 - - + -
256A LEU* 4.2 12.3 - - + -
264A VAL* 5.4 0.2 - - + -
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Residues in contact with ASP 89 (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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85A ARG* 2.9 23.0 + - - +
86A ALA 3.7 7.4 - - - +
88A LEU* 1.3 73.6 - - - +
90A ALA* 1.3 55.3 + - - +
91A HIS 2.8 10.0 - - - +
94A VAL 2.9 5.8 - - - +
95A ARG* 3.0 24.7 - - - +
96A CYS* 3.2 12.3 + - - +
97A GLY* 2.6 27.1 + - - -
275A GLY 2.7 28.2 - - - +
276A GLY 2.4 30.2 - - - +
277A VAL* 3.6 17.9 - - + -
278A SER* 4.2 3.1 + - - -
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Residues in contact with ALA 90 (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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86A ALA 3.3 8.3 + - - +
87A MET 3.8 7.9 - - - +
89A ASP* 1.3 77.1 - - - +
91A HIS* 1.3 65.6 + - - +
92A PRO* 3.3 6.9 - - - +
263A ALA* 4.2 12.8 - - - +
267A HIS* 4.0 16.2 - - + -
270A LEU* 3.4 35.0 - - + +
275A GLY 4.2 3.5 - - - +
276A GLY* 3.9 2.9 - - - -
277A VAL* 3.5 19.7 - - + +
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Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET 3.7 7.2 + - - +
88A LEU* 3.2 19.2 + - + +
89A ASP 2.8 7.3 - - - +
90A ALA* 1.3 76.0 - - - +
92A PRO* 1.3 71.7 - - + +
93A GLU* 3.2 60.0 + - + +
94A VAL* 2.7 37.0 + - + +
253A LEU* 4.6 20.6 - - + -
258A ILE* 3.5 13.4 - - + +
259A ALA 3.2 21.3 + - - -
261A SER* 3.7 24.9 - - - -
263A ALA* 4.9 1.5 - - - +
264A VAL* 5.1 5.1 - - + +
275A GLY 3.4 0.3 - - - +
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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