Contacts of the helix formed by residues 85 - 101 (chain A) in PDB entry 4GAB
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 GLU 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PHE 3.4 0.6 - - - -
84A PHE* 1.3 77.2 - - - +
86A ARG* 1.3 60.6 + - - +
87A PRO* 3.4 9.7 - - + +
88A LEU* 2.8 36.5 + - + +
89A VAL 2.9 10.4 + - - -
118A SER* 3.0 33.0 + - - -
135A LYS* 4.4 24.4 + - + +
136A ALA* 3.9 20.0 - - + +
140A ASP* 6.0 0.2 - - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.6 2.2 + - - -
85A GLU* 1.3 69.2 - - - +
87A PRO* 1.4 72.8 - - + +
89A VAL* 3.2 12.9 + - - +
90A ARG* 3.4 11.4 + - - +
140A ASP* 5.1 5.0 + - - +
143A GLU* 3.7 34.1 + - - +
144A ALA* 3.7 27.5 - - + +
147A GLU* 2.2 46.3 + - - +
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 3.6 10.5 - - + +
86A ARG* 1.4 94.7 - - + +
88A LEU* 1.3 64.7 - - + +
90A ARG* 3.5 7.6 + - + +
91A LYS* 3.1 34.6 + - + +
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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
----------------------------------------------------------
82A THR 4.0 9.2 - - - +
83A PHE* 3.7 26.7 - - + +
85A GLU* 2.8 29.7 + - + +
87A PRO* 1.3 82.0 - - + +
89A VAL* 1.3 61.9 + - - +
91A LYS* 3.7 13.1 - - + +
92A ALA* 2.8 34.0 + - - +
118A SER* 3.6 30.7 - - - -
119A GLY 5.5 0.7 - - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.0 20.7 - - + +
83A PHE 3.1 19.3 + - - +
84A PHE* 3.6 13.2 - - - +
85A GLU 2.9 14.7 + - - +
86A ARG 3.2 6.7 + - - +
88A LEU* 1.3 76.7 - - - +
90A ARG* 1.3 59.1 + - - +
92A ALA* 3.9 1.0 - - - +
93A PHE* 2.9 29.1 + - - +
108A TYR* 4.9 0.7 - - + -
141A ALA* 4.2 4.7 - - - -
144A ALA* 3.7 30.3 - - + +
145A MET* 3.9 24.7 - - + +
148A LEU* 4.8 7.4 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG 3.4 8.4 + - - +
87A PRO* 3.7 8.7 - - + +
88A LEU 3.2 0.4 - - - -
89A VAL* 1.3 82.2 - - - +
91A LYS* 1.3 61.0 + - + +
93A PHE* 3.4 4.1 + - - +
94A GLU* 2.8 66.0 + - - +
144A ALA* 4.8 1.8 + - - +
147A GLU* 3.8 22.6 + - - +
148A LEU* 3.4 26.4 - - - +
151A GLU* 2.9 44.1 + - - -
153A LEU* 3.8 15.4 - - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 6.2 0.9 - - + -
87A PRO* 3.1 25.7 + - + +
88A LEU* 3.7 16.8 - - + +
90A ARG* 1.3 81.5 - - - +
92A ALA* 1.3 61.9 + - - +
94A GLU* 3.4 22.5 + - - +
95A LYS* 3.1 23.9 + - - +
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Residues in contact with ALA 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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47A TYR* 3.9 18.7 - - + -
79A LEU* 3.9 16.2 - - + -
80A TRP 5.9 0.2 - - - +
83A PHE* 3.8 30.9 - - + -
88A LEU 2.8 20.0 + - - +
91A LYS* 1.3 69.9 - - - +
93A PHE* 1.3 68.2 + - - +
95A LYS* 3.3 3.8 + - - +
96A THR* 3.0 24.8 + - - -
108A TYR* 4.1 3.1 - - - +
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL 2.9 19.8 + - - +
90A ARG* 3.8 3.8 - - - +
92A ALA* 1.3 76.3 - - - +
94A GLU* 1.3 69.0 + - + +
96A THR* 3.1 5.9 + - + -
97A LEU* 2.8 55.5 + - + +
105A LEU* 3.7 19.7 - - + -
108A TYR* 3.5 28.0 + + - +
148A LEU* 3.7 32.3 - - + -
153A LEU* 3.7 36.8 - - + -
154A VAL* 3.4 29.2 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 2.8 49.2 + - - +
91A LYS* 3.7 28.6 + - - +
93A PHE* 1.3 84.7 - - + +
95A LYS* 1.3 56.9 + - - +
97A LEU* 3.9 5.3 - - + +
98A LYS* 2.9 31.0 + - - +
153A LEU* 6.1 2.0 - - + +
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Residues in contact with LYS 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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47A TYR* 3.7 27.4 + - + +
53A HIS* 5.9 0.8 + - - -
91A LYS 3.1 14.4 + - - +
92A ALA* 3.6 8.7 - - - +
94A GLU* 1.3 73.4 - - - +
96A THR* 1.3 60.7 + - - +
98A LYS* 3.8 6.0 - - + +
99A ASP* 2.7 67.1 + - - +
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Residues in contact with THR 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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47A TYR* 3.7 17.2 - - - +
52A GLU* 2.8 25.4 + - - +
77A SER* 3.4 32.4 + - - +
78A LYS 4.8 1.7 + - - -
92A ALA 3.0 14.5 + - - -
93A PHE* 3.4 10.8 - - - +
95A LYS* 1.3 78.5 - - - +
97A LEU* 1.3 56.9 + - - +
99A ASP* 3.3 2.5 + - - +
100A LEU* 2.9 37.9 + - + +
105A LEU* 4.2 11.2 - - + -
108A TYR* 4.8 5.5 + - + -
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Residues in contact with LEU 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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93A PHE* 2.8 49.3 + - + +
94A GLU* 4.0 6.1 - - + +
96A THR* 1.3 75.5 - - - +
98A LYS* 1.3 57.1 + - - +
100A LEU* 3.4 3.2 + - - -
101A LYS* 3.0 22.9 + - - -
102A LEU* 3.3 42.9 + - + +
103A SER* 4.1 12.8 - - - +
104A TYR* 3.8 27.8 - - - +
105A LEU* 4.1 9.2 - - + +
153A LEU* 4.6 9.9 - - + -
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Residues in contact with LYS 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 GLU 2.9 18.6 + - - +
95A LYS* 3.8 7.9 - - + +
97A LEU* 1.3 75.6 - - - +
99A ASP* 1.3 70.7 + - - +
101A LYS* 3.1 21.3 + - - +
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Residues in contact with ASP 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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52A GLU* 3.5 16.9 - - + +
53A HIS* 3.3 43.0 + - - +
56A GLY* 3.7 1.4 - - - -
95A LYS* 2.7 58.2 + - - +
96A THR* 3.7 4.0 - - - +
98A LYS* 1.3 80.0 - - - +
100A LEU* 1.3 59.6 + - - +
101A LYS* 3.1 25.1 + - - +
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Residues in contact with LEU 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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45A CYS* 4.1 9.2 - - - -
52A GLU* 3.5 33.4 - - + +
55A VAL* 3.8 24.9 - - + -
56A GLY* 3.3 16.3 - - - +
59A ILE* 4.9 4.4 - - + +
75A ILE* 4.0 13.2 - - + -
77A SER* 4.4 3.1 - - - -
96A THR* 2.9 31.3 + - + +
97A LEU* 4.0 2.9 - - - +
98A LYS 3.3 0.2 - - - -
99A ASP* 1.3 73.7 - - - +
101A LYS* 1.3 69.3 + - - +
102A LEU* 3.3 23.2 + - + +
105A LEU* 3.7 29.4 - - + -
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Residues in contact with LYS 101 (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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53A HIS* 3.3 23.4 + - - +
56A GLY 3.8 18.8 - - - +
57A GLU* 3.9 17.6 + - - +
60A GLN* 3.8 38.5 - - + +
97A LEU 3.0 6.1 + - - -
98A LYS* 3.1 14.6 + - - +
99A ASP* 3.1 18.9 + - - +
100A LEU* 1.3 78.3 - - - +
102A LEU* 1.3 62.0 + - - +
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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