Contacts of the helix formed by residues 77 - 94 (chain A) in PDB entry 2AGQ
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 ARG 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.7 33.9 + - - +
19A LEU* 3.5 28.8 - - - +
75A PRO* 3.6 15.9 + - + +
76A MET* 1.3 75.5 - - - +
78A LYS* 1.3 65.4 + - - +
79A GLU* 3.3 14.8 - - - +
80A VAL* 3.0 35.5 + - + +
81A TYR* 2.9 27.8 + - + +
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Residues in contact with LYS 78 (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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12A TYR* 3.3 30.5 - - + +
76A MET* 3.7 21.8 + - - +
77A ARG* 1.3 73.4 - - - +
79A GLU* 1.3 74.4 + - + +
81A TYR* 3.0 14.0 + - - +
82A GLN* 2.9 27.5 + - + +
104A ILE* 4.5 12.9 - - + +
5C G 5.5 6.4 + - - +
6C A 3.7 34.4 + - - -
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Residues in contact with GLU 79 (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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76A MET 4.8 1.7 - - - +
77A ARG* 3.6 18.2 - - - +
78A LYS* 1.3 92.0 + - + +
80A VAL* 1.3 64.1 + - + +
82A GLN* 3.4 8.2 + - - +
83A GLN* 3.0 35.3 + - + +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.2 14.1 - - + -
19A LEU* 3.9 26.9 - - + -
77A ARG* 3.0 40.3 + - + +
79A GLU* 1.3 82.4 - - + +
81A TYR* 1.3 66.8 + - + +
83A GLN* 3.1 10.5 + - - +
84A VAL* 3.0 25.5 + - + +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.4 22.6 - - + -
12A TYR* 3.4 63.0 - + + -
15A VAL* 3.7 24.5 - - + -
16A GLU* 2.7 34.8 + - - +
30A VAL* 3.9 5.4 - - - +
75A PRO 4.0 0.5 + - - -
76A MET* 3.7 8.5 - - + -
77A ARG* 2.9 46.2 + - + -
78A LYS* 3.0 9.8 + - - +
80A VAL* 1.3 76.9 - - + +
82A GLN* 1.3 51.8 + - - +
84A VAL* 3.4 5.9 + - - +
85A SER* 2.7 34.8 + - - -
104A ILE* 4.4 2.2 - - + -
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Residues in contact with GLN 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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78A LYS* 2.9 20.9 + - + +
79A GLU* 3.5 9.4 - - - +
81A TYR* 1.3 75.3 - - - +
83A GLN* 1.3 61.6 + - + +
85A SER* 3.2 13.5 + - - -
86A SER* 2.8 44.2 + - - +
104A ILE* 3.8 23.8 - - + +
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Residues in contact with GLN 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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79A GLU* 3.0 23.0 + - - +
80A VAL* 3.1 9.1 + - - +
82A GLN* 1.3 73.0 - - + +
84A VAL* 1.3 67.6 + - + +
86A SER* 3.3 7.3 + - - -
87A ARG* 3.2 39.9 + - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.3 2.2 - - + -
15A VAL* 4.0 33.7 - - + -
19A LEU* 5.3 6.7 - - + -
80A VAL* 3.0 18.9 + - + +
81A TYR* 3.7 8.5 - - - +
83A GLN* 1.3 78.1 - - + +
85A SER* 1.3 63.4 + - - +
87A ARG* 3.1 40.5 + - - +
88A ILE* 3.1 28.2 + - + +
136A GLU* 4.6 7.4 - - - +
138A ILE* 4.6 9.2 - - + -
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Residues in contact with SER 85 (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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8A PHE* 4.4 5.6 - - - -
11A PHE* 3.9 11.2 - - - -
81A TYR 2.7 21.5 + - - -
82A GLN* 3.4 9.7 + - - -
84A VAL* 1.3 74.3 - - - +
86A SER* 1.3 64.4 + - - +
88A ILE* 3.0 5.0 + - - +
89A MET* 3.0 34.4 + - - +
104A ILE* 2.5 42.4 + - - +
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Residues in contact with SER 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 GLN* 2.8 37.5 + - - +
83A GLN* 3.7 8.2 - - - -
84A VAL 3.3 0.2 - - - -
85A SER* 1.3 73.6 + - - +
87A ARG* 1.3 62.2 + - - +
89A MET* 3.5 8.8 + - - +
90A ASN* 3.3 29.8 + - - -
93A ARG* 5.6 0.2 + - - -
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Residues in contact with ARG 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 GLN* 3.2 33.4 + - - +
84A VAL* 3.1 29.8 + - - +
86A SER* 1.3 74.5 - - - +
88A ILE* 1.3 66.9 + - - +
90A ASN* 3.3 12.1 + - - +
91A LEU* 3.3 24.4 + - - +
136A GLU* 2.9 43.8 + - - +
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Residues in contact with ILE 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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8A PHE* 3.4 43.3 - - + -
11A PHE* 4.4 1.8 - - + -
84A VAL* 3.1 20.3 + - + +
85A SER 3.0 6.1 + - - +
87A ARG* 1.3 74.0 - - - +
89A MET* 1.3 65.9 - - - +
91A LEU* 2.9 20.4 + - - +
92A LEU* 3.1 14.4 + - + +
132A ILE* 3.8 29.4 - - + -
136A GLU* 4.3 16.8 - - + -
138A ILE* 4.0 37.5 - - + -
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Residues in contact with MET 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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8A PHE* 3.6 23.1 - - + -
85A SER* 3.0 21.1 + - - +
86A SER* 3.7 11.9 - - - +
87A ARG 3.3 0.2 - - - -
88A ILE* 1.3 76.9 - - - +
90A ASN* 1.3 62.0 + - - +
92A LEU* 3.0 18.6 + - - +
93A ARG* 3.1 22.7 + - - +
99A ILE* 4.6 2.3 - - + +
101A ILE* 3.8 35.9 - - + -
103A SER 3.5 17.3 - - - +
104A ILE 3.5 24.5 - - - +
106A GLU 3.8 13.9 - - - +
107A ALA* 4.2 18.2 - - - -
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Residues in contact with ASN 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 SER* 3.3 18.2 + - - +
87A ARG* 3.6 12.0 - - - +
88A ILE 3.2 0.6 - - - -
89A MET* 1.3 77.3 - - - +
91A LEU* 1.3 62.6 + - + +
93A ARG* 2.8 43.2 + - - +
94A GLU* 3.9 13.2 - - - +
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Residues in contact with LEU 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 ARG 3.3 14.2 + - - +
88A ILE* 2.9 16.2 + - - +
90A ASN* 1.3 78.4 - - + +
92A LEU* 1.3 63.0 + - - +
94A GLU* 3.4 14.4 + - + +
95A TYR* 3.2 21.7 - - + -
131A LYS* 4.5 15.7 - - + +
132A ILE* 4.0 27.4 - - + -
135A LYS* 3.8 45.5 - - + -
136A GLU* 4.3 10.1 - - + +
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Residues in contact with LEU 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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6A VAL* 4.0 24.5 - - + -
8A PHE* 4.8 1.3 - - + -
88A ILE* 3.6 17.0 - - + +
89A MET* 3.0 18.4 + - - +
91A LEU* 1.3 74.3 - - - +
93A ARG* 1.3 57.4 + - - +
94A GLU 3.0 2.9 - - - -
95A TYR* 2.9 29.4 + - + +
96A SER 3.8 0.7 + - - -
99A ILE* 3.6 13.6 - - + +
107A ALA* 3.6 28.9 - - + -
109A LEU* 3.6 12.3 - - + +
128A ILE* 3.4 38.4 - - + -
132A ILE* 3.9 13.2 - - + -
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Residues in contact with ARG 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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86A SER 5.6 0.2 + - - -
89A MET* 3.1 14.2 + - - +
90A ASN* 2.8 40.3 + - - +
91A LEU 3.3 0.6 - - - -
92A LEU* 1.3 75.1 - - - +
94A GLU* 1.3 66.3 + - - +
95A TYR 3.0 1.7 + - - -
96A SER 3.2 25.2 + - - +
97A GLU* 5.0 2.4 - - - +
99A ILE* 4.4 25.0 - - + +
101A ILE* 3.3 32.1 - - - +
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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
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90A ASN 3.9 12.9 - - - +
91A LEU* 3.5 18.8 - - + +
92A LEU 3.0 0.6 + - - -
93A ARG* 1.3 82.3 - - - +
95A TYR* 1.3 68.1 + - + +
96A SER 3.5 0.4 - - - -
97A GLU* 6.1 0.4 - - - -
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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