Contacts of the helix formed by residues 83 - 100 (chain A) in PDB entry 3A4Y
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LEU 5.1 0.4 + - - -
82A ALA* 1.3 76.6 - - - +
84A ARG* 1.3 66.5 + - - +
85A ALA 3.5 0.3 + - - -
86A THR* 3.0 16.3 + - - -
87A VAL* 2.9 18.9 + - - +
121A LEU 3.3 17.7 - - - +
122A GLU* 3.7 17.7 - - - +
123A TYR* 4.1 20.6 - - + -
136A PHE* 4.0 13.3 - - + -
144A GLY* 2.9 32.2 + - - +
146A ALA* 5.2 0.4 - - + -
267A TYR* 3.9 6.5 - - - -
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Residues in contact with ARG 84 (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 ALA 3.8 0.2 + - - -
83A THR* 1.3 72.2 - - - +
85A ALA* 1.3 57.1 + - - +
87A VAL* 3.1 11.6 + - - +
88A LEU* 2.8 37.0 + - + +
120A PRO* 3.3 38.1 + - + +
122A GLU* 2.9 44.8 + - - +
125A GLU* 5.5 3.0 + - - -
266A ARG* 3.8 3.7 - - - +
267A TYR* 3.2 10.7 + - + +
432A SO4 3.2 41.3 + - - +
270D GLU* 2.5 40.5 + - - +
437D SO4 3.5 17.8 + - - -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR 3.1 0.6 - - - -
84A ARG* 1.3 78.1 - - - +
86A THR* 1.3 57.0 + - - +
88A LEU* 3.4 1.4 + - - +
89A LEU* 2.9 34.4 + - - +
143A PRO* 3.5 11.0 - - + +
144A GLY* 3.5 23.3 - - - -
264A LEU* 4.2 16.8 - - + +
267A TYR* 3.3 35.8 + - + -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.6 4.5 + - + -
58A THR 4.3 1.2 + - - -
59A HIS* 3.4 21.4 - - - +
60A ALA* 3.2 32.4 + - - +
82A ALA* 3.9 14.1 - - + +
83A THR* 3.0 20.1 + - - -
85A ALA* 1.3 74.7 - - - +
87A VAL* 1.3 58.8 + - - +
89A LEU* 4.3 1.8 - - - -
90A MET* 2.7 51.8 + - + +
143A PRO 4.4 1.6 + - - -
144A GLY 3.3 14.0 + - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 3.8 18.6 - - + +
83A THR 2.9 22.0 + - - +
84A ARG* 3.1 11.4 + - + +
86A THR* 1.3 78.3 - - - +
88A LEU* 1.3 72.6 + - + +
90A MET* 3.5 19.1 + - - +
91A GLU* 3.6 7.1 + - - +
118A LEU* 3.8 36.1 - - + +
119A ARG 4.9 1.6 - - - +
120A PRO* 4.8 11.9 - - + -
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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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84A ARG* 2.8 22.1 + - + +
85A ALA 4.0 2.9 - - - +
87A VAL* 1.3 80.5 - - + +
89A LEU* 1.3 61.0 + - - +
91A GLU* 3.4 25.9 + - - +
92A ILE* 3.9 5.9 + - - +
260A LEU* 4.0 24.2 - - + +
263A ARG* 3.6 39.9 - - - +
264A LEU* 3.9 20.2 - - + -
432A SO4 3.7 23.3 - - - +
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Residues in contact with LEU 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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60A ALA* 3.3 23.8 - - + +
85A ALA 2.9 19.2 + - - +
86A THR* 4.9 0.4 - - - -
88A LEU* 1.3 75.9 - - - +
90A MET* 1.3 64.4 + - - +
92A ILE* 2.9 17.2 + - + +
93A VAL* 3.0 18.1 + - + +
142A LEU* 5.2 7.2 - - + -
143A PRO* 3.8 39.5 - - + +
225A VAL* 5.0 10.5 - - + -
257A VAL* 4.1 33.9 - - + -
260A LEU* 4.1 18.4 - - + -
261A TYR* 5.3 1.8 - - + -
264A LEU* 4.7 7.0 - - + -
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Residues in contact with MET 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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57A LEU* 3.4 27.6 - - + -
60A ALA* 3.6 8.2 - - + +
65A VAL* 4.0 28.3 - - + -
68A LEU* 4.4 9.9 - - - -
82A ALA* 4.2 4.0 - - + -
86A THR* 2.7 30.2 + - + +
87A VAL* 3.5 16.8 - - - +
89A LEU* 1.3 72.2 - - - +
91A GLU* 1.3 54.3 + - - +
93A VAL* 3.8 4.4 - - - +
94A LEU* 2.7 47.9 + - + +
115A LEU* 4.6 4.5 - - + -
118A LEU* 3.4 34.5 - - + -
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Residues in contact with GLU 91 (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 VAL 3.6 6.6 + - - +
88A LEU* 3.4 19.0 + - - +
89A LEU 3.1 1.0 + - - -
90A MET* 1.3 79.6 - - - +
92A ILE* 1.3 58.7 + - + +
94A LEU* 4.8 0.2 - - - -
95A GLU* 2.8 49.2 + - + +
115A LEU* 3.8 32.6 - - + +
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Residues in contact with ILE 92 (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 LEU 4.2 5.6 - - - +
89A LEU* 2.9 7.6 + - + +
91A GLU* 1.3 75.9 - - + +
93A VAL* 1.3 62.2 + - + +
95A GLU* 4.1 3.3 - - - +
96A ASP* 2.9 34.5 + - - +
253A MET* 3.9 21.5 - - + -
256A ARG* 4.1 44.9 - - + +
257A VAL* 4.2 14.8 - - + -
260A LEU* 3.6 34.1 - - + -
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Residues in contact with VAL 93 (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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60A ALA* 3.4 30.1 - - + +
61A ALA* 5.0 0.2 - - - -
62A LEU* 3.2 39.3 - - + +
65A VAL* 4.4 4.0 - - + -
89A LEU* 3.0 19.6 + - + +
90A MET* 3.8 7.0 - - - +
92A ILE* 1.3 77.2 - - + +
94A LEU* 1.3 56.8 + - - +
96A ASP* 3.8 2.9 - - - +
97A ALA* 2.9 27.0 + - - +
225A VAL* 4.2 24.7 - - + -
253A MET* 4.3 12.0 - - + +
257A VAL* 6.0 1.1 - - + -
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Residues in contact with LEU 94 (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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62A LEU* 4.2 12.1 - - + -
65A VAL* 4.0 30.3 - - + +
66A GLY* 4.6 4.3 - - - +
68A LEU* 5.2 5.4 - - + -
69A PRO* 4.6 24.2 - - + -
90A MET* 2.7 36.8 + - + +
91A GLU* 4.3 2.0 - - - +
93A VAL* 1.3 72.5 - - - +
95A GLU* 1.3 67.0 - - - +
97A ALA* 2.9 6.2 + - + +
98A LEU* 2.9 22.7 + - - +
106A PHE* 5.0 5.2 - - + -
111A VAL* 3.8 24.6 - - + +
114A ALA* 5.3 2.9 - - + -
115A LEU* 4.2 19.5 - - + -
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Residues in contact with GLU 95 (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 GLU* 2.8 43.0 + - + +
92A ILE* 4.1 3.1 - - - +
94A LEU* 1.3 76.2 - - - +
96A ASP* 1.3 63.5 + - - +
98A LEU* 3.2 25.0 + - - +
99A LYS* 3.2 13.9 + - - +
111A VAL* 4.5 10.5 - - - +
115A LEU* 4.2 15.0 - - + +
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Residues in contact with ASP 96 (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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62A LEU* 5.8 2.6 - - - +
92A ILE* 2.9 20.3 + - + +
93A VAL 3.8 1.4 - - - +
95A GLU* 1.3 77.5 - - - +
97A ALA* 1.3 60.0 + - - +
99A LYS* 3.1 9.8 + - - +
100A VAL* 2.8 42.6 + - - +
253A MET* 3.2 35.7 - - + +
256A ARG* 3.4 23.6 + - - +
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Residues in contact with ALA 97 (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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32A MET* 4.7 1.6 - - + -
62A LEU* 3.7 27.6 - - + -
93A VAL 2.9 18.5 + - - +
94A LEU* 2.9 8.1 + - + +
96A ASP* 1.3 79.8 + - - +
98A LEU* 1.3 61.4 + - - +
100A VAL* 2.7 24.9 - - - +
101A MET* 3.3 28.2 - - + +
106A PHE* 4.7 6.5 - - + -
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Residues in contact with LEU 98 (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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94A LEU 2.9 11.0 + - - +
95A GLU* 3.5 20.4 - - - +
96A ASP 3.1 0.4 - - - -
97A ALA* 1.3 78.6 - - - +
99A LYS* 1.3 63.7 + - - +
100A VAL 4.3 2.1 - - - -
101A MET* 4.5 6.0 + - - +
104A PRO* 5.1 11.5 - - + +
106A PHE* 3.8 36.0 - - + +
107A GLY* 4.5 0.2 - - - -
108A PRO* 3.4 46.7 - - + -
111A VAL* 3.7 12.6 - - + -
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Residues in contact with LYS 99 (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 GLU 3.2 7.7 + - - +
96A ASP* 3.1 12.5 + - - +
98A LEU* 1.3 82.2 - - - +
100A VAL* 1.3 64.1 + - + +
101A MET 3.8 3.5 + - - +
256A ARG* 5.8 4.2 - - - +
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Residues in contact with VAL 100 (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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96A ASP* 2.8 33.1 + - - +
97A ALA* 2.7 21.6 - - - +
99A LYS* 1.3 83.8 - - + +
101A MET* 1.3 67.5 + - - +
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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