Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 1GC5
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 SER 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ILE 3.6 2.8 + - - -
76A SER* 3.7 25.3 - - - +
99A VAL* 3.6 4.6 - - - +
100A GLU* 1.3 79.9 - - - +
102A GLU* 1.3 61.6 + - - +
103A GLU* 3.3 8.5 + - - +
104A VAL* 2.6 45.8 + - - +
105A ARG* 3.0 19.8 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLU 3.7 4.1 + - - +
101A SER* 1.3 71.7 - - - +
103A GLU* 1.3 62.2 + - - +
105A ARG* 3.0 42.7 + - - +
106A ARG* 3.1 45.8 + - - +
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Residues in contact with GLU 103 (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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59A LYS* 5.5 0.3 + - - -
78A ILE* 3.5 30.1 - - - +
101A SER* 3.6 9.2 - - - +
102A GLU* 1.3 77.7 - - - +
104A VAL* 1.3 65.0 + - + +
106A ARG* 3.3 15.4 + - - +
107A TYR* 3.2 17.7 + - - +
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Residues in contact with VAL 104 (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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75A ILE* 3.8 13.2 - - + -
76A SER 4.1 0.2 - - - -
77A SER* 3.4 36.1 - - - +
78A ILE* 3.8 11.0 - - + +
81A LEU* 4.1 22.4 - - + -
99A VAL* 3.5 23.6 - - + -
101A SER* 2.6 33.6 + - - +
103A GLU* 1.3 70.3 - - + +
105A ARG* 1.3 58.3 + - - +
107A TYR* 2.8 25.3 + - + +
108A LEU* 2.9 17.8 + - + +
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Residues in contact with ARG 105 (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 PHE* 3.4 10.9 - - - -
99A VAL* 2.9 32.6 + - + +
100A GLU* 4.8 4.4 + - - +
101A SER 3.0 15.6 + - - +
102A GLU* 3.0 44.9 + - - +
104A VAL* 1.3 77.9 - - - +
106A ARG* 1.3 60.8 + - - +
108A LEU* 3.5 10.6 + - + +
109A ARG* 3.3 25.6 + - - +
180A GLU* 5.5 1.2 + - - -
185A TYR* 4.1 4.4 + - + -
210A ALA* 3.8 37.8 + - + +
212A ASP* 2.7 42.2 + - - -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.1 35.1 + - - +
103A GLU* 3.6 15.3 - - - +
104A VAL 3.2 0.4 - - - -
105A ARG* 1.3 73.8 - - - +
107A TYR* 1.3 68.6 + - - +
109A ARG* 3.5 8.2 + - - +
110A GLU* 3.2 29.4 + - - +
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Residues in contact with TYR 107 (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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55A ARG* 3.3 43.6 + - - +
58A GLU* 5.2 4.1 + - - -
59A LYS* 3.4 27.3 - - - -
78A ILE* 3.5 24.7 - - + -
81A LEU* 3.6 23.1 - - + -
82A LEU* 4.0 10.9 - - + +
103A GLU* 3.2 8.4 + - - +
104A VAL* 2.8 19.2 + - - +
106A ARG* 1.3 78.9 - - - +
108A LEU* 1.3 55.8 + - - +
110A GLU* 3.1 10.2 + - + +
111A TRP* 2.9 55.4 + + - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.6 35.0 - - + -
99A VAL* 3.9 29.6 - - + -
104A VAL* 2.9 19.0 + - + +
105A ARG* 3.6 13.0 - - - +
107A TYR* 1.3 76.9 - - + +
109A ARG* 1.3 61.8 + - - +
111A TRP* 3.3 9.4 + - - +
112A GLY* 3.0 19.1 + - - +
185A TYR* 3.4 45.9 - - + -
187A TYR* 3.3 21.5 + - - +
208A ALA* 4.2 6.7 - - + -
210A ALA* 4.7 2.2 - - + -
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Residues in contact with ARG 109 (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 ARG* 3.3 15.5 + - - +
106A ARG* 4.0 7.9 - - - +
107A TYR 3.3 1.0 - - - -
108A LEU* 1.3 75.7 - - - +
110A GLU* 1.3 63.2 + - + +
112A GLY* 2.8 21.5 + - - -
113A TRP* 4.5 20.2 - - + -
181A GLU* 3.0 30.3 + - - +
183A ILE* 3.8 16.5 - - - +
185A TYR* 3.7 16.1 + - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 5.3 1.3 + - - -
106A ARG* 3.2 16.3 + - + +
107A TYR* 3.1 11.8 + - + +
109A ARG* 1.3 80.6 - - + +
111A TRP* 1.3 64.7 + - - +
112A GLY* 3.1 1.4 + - - -
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Residues in contact with TRP 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LYS* 2.6 62.1 + - + +
47A LEU* 4.3 17.9 - - + -
51A ASP* 2.8 23.5 + - - -
52A LEU* 4.1 12.1 - - + -
55A ARG* 3.0 47.1 + - - +
81A LEU* 4.3 4.7 - - + -
82A LEU* 3.8 31.0 - - + -
85A ILE* 3.8 22.0 - - + -
107A TYR* 2.9 30.9 + + + +
108A LEU* 3.4 10.3 - - + +
110A GLU* 1.3 77.2 - - - +
112A GLY* 1.3 57.1 + - - +
187A TYR* 3.6 25.4 - + - +
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Residues in contact with GLY 112 (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 LYS* 3.2 22.2 - - - +
108A LEU 3.0 10.0 + - - +
109A ARG 2.8 17.8 + - - -
110A GLU 4.0 0.9 - - - -
111A TRP* 1.3 79.9 - - - +
113A TRP* 1.3 70.4 + - - +
185A TYR* 5.0 3.3 - - - -
187A TYR* 4.9 3.8 + - - -
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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