Contacts of the helix formed by residues 89 - 105 (chain A) in PDB entry 2HGK
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 GLN 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A HIS* 5.0 14.7 + - + -
87A HIS* 2.9 34.5 + - + +
88A PRO* 1.3 78.8 - - + +
90A ARG* 1.3 59.4 + - - +
91A ALA* 3.0 7.2 + - - -
92A LEU* 3.2 33.9 + - + +
93A ILE* 4.2 4.4 + - - +
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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
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80A GLU* 2.7 44.8 + - - +
83A LEU* 2.8 53.1 + - + -
84A ALA 3.7 14.8 - - - -
85A THR* 3.5 32.2 + - - +
87A HIS* 2.8 19.6 + - + +
88A PRO* 2.9 4.8 - - + +
89A GLN* 1.3 75.4 - - - +
91A ALA* 1.3 56.5 + - - +
92A LEU 3.1 0.2 - - - -
93A ILE* 3.0 11.8 + - - +
94A LEU* 2.8 55.9 + - + +
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Residues in contact with ALA 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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88A PRO 3.3 14.5 + - - +
89A GLN* 3.0 0.9 - - - -
90A ARG* 1.3 82.8 - - + +
92A LEU* 1.3 55.9 + - + +
94A LEU* 3.8 9.8 - - - +
95A ALA* 2.8 36.4 + - - +
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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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17A LEU* 3.6 14.6 - - + +
21A HIS* 3.9 31.4 - - + +
89A GLN* 3.2 24.9 + - + +
90A ARG 3.1 0.4 - - - -
91A ALA* 1.3 79.4 - - + +
93A ILE* 1.3 62.9 + - + +
95A ALA* 3.5 5.1 + - - +
96A GLU* 3.3 26.5 + - - +
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Residues in contact with ILE 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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14A LEU* 4.6 9.0 - - + -
17A LEU* 3.8 26.5 - - + -
18A LEU* 5.5 6.3 - - + -
21A HIS* 6.6 0.2 - - + -
51A LEU* 4.4 16.8 - - + -
79A TYR* 6.2 1.6 - - + -
83A LEU* 4.0 25.8 - - + -
87A HIS* 6.5 0.4 - - + -
89A GLN 4.6 6.1 - - - +
90A ARG* 3.0 11.4 + - - +
92A LEU* 1.3 74.9 - - + +
94A LEU* 1.3 60.5 + - + +
96A GLU* 3.1 5.9 + - - +
97A LEU* 2.8 46.6 + - + +
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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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76A ALA* 4.1 19.3 - - + +
79A TYR* 4.2 7.0 - - + +
80A GLU* 4.1 18.2 - - + +
83A LEU* 5.6 2.7 - - + -
90A ARG* 2.8 62.7 + - + +
91A ALA* 3.8 7.9 - - - +
93A ILE* 1.3 74.6 - - + +
95A ALA* 1.3 51.8 + - - +
97A LEU* 3.1 21.0 + - + +
98A GLU* 2.7 49.9 + - + +
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Residues in contact with ALA 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 ALA 2.8 22.1 + - - +
92A LEU* 3.7 7.6 - - + +
94A LEU* 1.3 72.6 - - - +
96A GLU* 1.3 59.7 + - + +
98A GLU* 3.9 12.2 + - - +
99A LYS* 3.0 30.7 + - - +
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Residues in contact with GLU 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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10A GLN* 2.7 38.5 + - - +
13A ALA* 3.8 20.2 - - - +
14A LEU* 4.2 19.6 + - + -
17A LEU* 3.7 18.7 - - + +
92A LEU 3.3 12.5 + - - +
93A ILE 3.1 9.0 + - - +
95A ALA* 1.3 77.9 - - + +
97A LEU* 1.3 59.3 + - - +
99A LYS* 2.8 32.6 + - - +
100A LEU* 2.9 28.2 + - - +
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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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14A LEU* 4.7 8.5 - - + -
51A LEU* 3.6 35.7 - - + -
75A VAL* 3.8 11.4 - - + -
76A ALA* 3.8 17.3 - - + +
79A TYR* 3.7 36.6 - - + -
93A ILE* 2.8 30.7 + - + +
94A LEU* 3.4 19.3 - - + +
96A GLU* 1.3 73.8 - - - +
98A GLU* 1.3 55.7 + - - +
99A LYS 3.0 1.3 - - - -
100A LEU* 3.0 10.0 + - + +
101A ASP* 2.7 40.2 + - - -
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Residues in contact with GLU 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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76A ALA* 3.6 22.0 - - + -
94A LEU* 2.7 34.6 + - + +
95A ALA* 4.0 9.3 - - - +
97A LEU* 1.3 71.9 - - - +
99A LYS* 1.3 56.3 + - - +
101A ASP* 4.0 4.9 - - - +
102A ALA* 3.0 28.1 + - - +
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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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10A GLN* 3.0 20.0 - - - +
13A ALA* 4.9 5.1 - - - +
95A ALA 3.0 18.2 + - - +
96A GLU* 2.8 41.0 + - - +
97A LEU 3.0 0.2 - - - -
98A GLU* 1.3 75.9 - - - +
100A LEU* 1.3 64.2 + - - +
102A ALA* 3.3 9.3 + - + +
103A LEU* 3.3 27.5 + - + +
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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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7A VAL* 4.2 12.6 - - + -
10A GLN* 3.4 29.5 + - + +
11A LEU* 4.2 18.6 - - + -
14A LEU* 5.3 7.6 - - + -
55A LEU* 4.3 18.4 - - + -
59A MET* 6.3 0.4 - - + -
73A PHE* 4.2 18.6 - - + -
75A VAL* 4.6 9.0 - - + -
96A GLU 2.9 14.3 + - - +
97A LEU* 3.3 13.7 - - + +
99A LYS* 1.3 73.4 - - - +
101A ASP* 1.3 60.7 + - - +
103A LEU* 2.8 22.3 + - + +
104A PHE* 3.1 40.2 - - + -
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Residues in contact with ASP 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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73A PHE* 3.5 21.9 - - - +
74A ALA* 3.2 15.7 - - + +
75A VAL* 2.9 29.2 + - - +
76A ALA* 2.8 38.9 + - - +
77A PRO* 4.0 0.2 - - - +
97A LEU 2.7 17.5 + - - +
98A GLU* 4.0 5.8 - - - +
100A LEU* 1.3 73.7 - - - +
102A ALA* 1.3 56.6 + - - +
104A PHE* 3.2 6.7 + - - +
105A ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 102 (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 GLU 3.0 21.4 + - - +
99A LYS* 3.4 11.4 - - + +
100A LEU 3.1 0.4 - - - -
101A ASP* 1.3 75.1 - - - +
103A LEU* 1.3 59.4 + - + +
105A ALA* 3.6 7.8 - - - +
106A ASP* 3.1 25.5 + - - +
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Residues in contact with LEU 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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3A THR* 5.7 0.9 - - - +
6A ARG* 4.4 9.0 - - + +
7A VAL* 3.9 33.0 - - + +
10A GLN* 3.6 39.7 - - + +
69A LEU* 3.6 11.2 - - - +
99A LYS* 3.3 14.8 - - + +
100A LEU 2.8 8.5 + - - +
102A ALA* 1.3 80.2 - - + +
104A PHE* 1.3 61.5 + - + +
105A ALA 3.2 0.2 - - - -
106A ASP* 3.1 28.3 + - + +
107A ASP* 3.4 6.6 + - - +
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Residues in contact with PHE 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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7A VAL* 4.3 15.3 - - + -
59A MET* 3.9 35.4 - - + -
69A LEU* 3.7 25.2 - - + +
70A PRO* 3.4 60.1 - - + +
71A GLY* 3.8 10.0 - - - -
73A PHE* 3.4 30.7 - + + +
100A LEU* 3.1 47.3 + - + -
101A ASP 3.2 6.4 + - - +
103A LEU* 1.3 77.9 - - + +
105A ALA* 1.3 56.9 + - - +
106A ASP 3.1 4.2 + - - -
107A ASP 3.8 11.8 - - - +
108A ALA* 5.5 0.5 - - - -
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Residues in contact with ALA 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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71A GLY* 4.0 13.4 + - - +
73A PHE 5.6 1.6 - - - +
101A ASP 2.9 17.0 + - - +
102A ALA* 3.6 9.2 - - - +
103A LEU 3.2 0.4 - - - -
104A PHE* 1.3 75.6 - - - +
106A ASP* 1.3 60.0 + - - +
107A ASP 5.2 0.4 - - - -
108A ALA* 5.6 3.0 - - - +
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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