Contacts of the helix formed by residues 77 - 92 (chain A) in PDB entry 2RHG
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL* 5.5 0.2 - - - -
53A PRO* 6.1 0.9 - - - -
72A PHE* 6.0 0.2 - - - -
75A GLY 3.5 11.7 - - - +
76A VAL* 1.3 81.0 - - - +
78A PRO* 1.3 77.2 - - + +
79A ALA* 3.7 7.5 + - - +
80A GLN* 2.9 38.8 + - - +
81A CYS* 3.0 16.3 + - - -
291B ASP* 3.7 11.0 - - - +
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Residues in contact with PRO 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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52A VAL* 4.2 18.4 - - + -
53A PRO 4.9 1.3 - - - +
72A PHE* 6.1 0.2 - - + -
77A THR* 1.3 81.9 - - - +
79A ALA* 1.3 60.9 + - - +
81A CYS* 3.0 19.2 + - + +
82A PHE* 3.1 28.8 + - + -
101A MET* 6.4 0.2 - - + -
105A LEU* 4.2 19.1 - - + -
291B ASP* 3.0 32.5 - - - +
293B GLN* 4.2 23.6 - - - +
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Residues in contact with ALA 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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77A THR* 3.1 8.9 + - - +
78A PRO* 1.3 80.3 - - - +
80A GLN* 1.3 61.9 + - + +
82A PHE* 3.5 10.5 + - - +
83A GLU* 3.0 33.4 + - - +
117A ARG* 5.1 1.2 + - - -
291B ASP* 4.7 7.7 + - - +
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Residues in contact with GLN 80 (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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30A ILE* 3.7 30.7 - - + +
75A GLY 2.8 27.4 + - - +
76A VAL* 3.1 16.4 - - + -
77A THR* 2.9 20.3 + - - +
79A ALA* 1.3 75.2 - - + +
81A CYS* 1.3 65.8 + - - +
83A GLU* 3.2 23.5 + - - +
84A MET* 3.0 27.4 + - + +
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Residues in contact with CYS 81 (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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25A LEU* 3.8 28.3 - - + +
52A VAL* 3.9 18.2 - - + -
53A PRO* 3.9 20.6 - - - -
76A VAL* 3.8 20.2 - - - -
77A THR 3.0 17.1 + - - -
78A PRO* 3.0 10.1 + - + +
80A GLN* 1.3 77.4 - - - +
82A PHE* 1.3 58.0 + - + +
84A MET* 3.0 9.9 + - - +
85A LEU* 2.8 34.8 + - + +
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Residues in contact with PHE 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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52A VAL* 6.1 3.8 - - + -
78A PRO* 3.1 31.6 + - + -
79A ALA* 3.9 8.1 - - - +
80A GLN 3.3 0.2 - - - -
81A CYS* 1.3 81.1 - - + +
83A GLU* 1.3 60.8 + - - +
85A LEU* 3.5 22.2 + - + -
86A ALA* 3.1 19.4 + - - +
99A LEU* 4.7 3.1 - - + -
101A MET* 5.9 1.3 - - + -
114A PHE* 3.3 41.3 - + - -
117A ARG* 3.5 53.7 + - + +
118A CYS* 4.1 19.5 - - - -
121A VAL* 3.6 21.1 - - + +
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Residues in contact with GLU 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 ALA* 3.0 26.8 - - - +
80A GLN* 3.3 24.6 + - - +
81A CYS 3.1 0.2 - - - -
82A PHE* 1.3 74.0 - - - +
84A MET* 1.3 66.3 + - + +
86A ALA* 3.5 6.7 + - - +
87A LEU* 3.1 30.3 + - + +
117A ARG* 5.1 7.6 - - - +
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Residues in contact with MET 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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25A LEU* 4.2 22.4 - - + -
26A GLY* 3.9 17.7 - - - +
30A ILE* 3.7 37.2 - - + +
33A SER* 3.5 34.8 - - - +
34A LEU* 3.7 21.1 - - + +
37A ILE* 4.9 0.9 - - + -
76A VAL* 5.6 1.8 - - - -
80A GLN 3.0 15.2 + - - +
81A CYS* 3.0 10.7 + - - +
83A GLU* 1.3 75.4 - - + +
85A LEU* 1.3 60.3 + - - +
87A LEU* 2.9 13.9 + - + +
88A ILE* 2.8 33.8 + - + +
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Residues in contact with LEU 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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25A LEU* 4.0 12.8 - - + -
50A LEU* 3.7 23.6 - - + -
52A VAL* 5.7 1.8 - - + -
81A CYS* 2.8 21.7 + - + +
82A PHE* 3.6 31.6 - - + +
84A MET* 1.3 76.5 - - - +
86A ALA* 1.3 60.9 + - - +
88A ILE* 3.3 6.5 + - + +
89A ARG* 3.0 24.6 + - - +
97A ILE* 4.2 13.5 - - + +
99A LEU* 3.7 36.8 - - + -
121A VAL* 3.9 12.5 - - + +
123A VAL* 4.0 12.3 - - + -
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Residues in contact with ALA 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 PHE 3.1 17.2 + - - +
83A GLU* 3.8 6.7 - - - +
85A LEU* 1.3 76.1 - - - +
87A LEU* 1.3 64.2 + - + +
89A ARG* 3.5 2.3 + - - +
90A GLU* 3.1 24.3 + - - +
117A ARG* 6.1 0.9 - - - +
121A VAL* 4.0 25.3 - - + +
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Residues in contact with LEU 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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30A ILE* 6.3 0.7 - - + -
34A LEU* 4.1 30.7 - - + -
83A GLU* 3.1 20.2 + - + +
84A MET* 2.9 11.7 + - + +
86A ALA* 1.3 77.0 - - + +
88A ILE* 1.3 64.6 + - - +
90A GLU* 3.3 14.9 + - + +
91A LYS* 3.3 24.7 + - - +
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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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25A LEU* 4.3 6.5 - - + -
34A LEU* 3.8 16.2 - - + -
37A ILE* 3.4 46.4 - - + -
38A ASP* 5.8 0.7 - - - +
41A ILE* 4.8 0.4 - - + -
48A LEU* 4.5 6.7 - - + -
50A LEU* 4.1 17.3 - - + -
84A MET 2.8 24.6 + - - +
85A LEU* 3.7 7.0 - - - +
87A LEU* 1.3 76.4 - - - +
89A ARG* 1.3 62.7 + - - +
91A LYS* 3.2 10.4 + - - +
92A HIS* 3.0 41.7 + - + +
95A ILE* 5.5 0.2 - - + -
97A ILE* 3.7 20.2 - - + -
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Residues in contact with ARG 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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3A ARG* 3.2 32.9 - - - +
85A LEU 3.0 10.7 + - - +
86A ALA 3.9 2.9 - - - +
87A LEU 3.3 0.2 - - - -
88A ILE* 1.3 76.9 - - - +
90A GLU* 1.3 61.8 + - - +
92A HIS 2.8 43.3 + - - +
93A PRO* 3.4 11.8 + - - +
95A ILE* 2.8 22.8 + - - +
97A ILE* 3.5 23.2 - - + +
121A VAL 3.3 25.4 - - - +
122A GLY* 2.9 25.6 + - - -
124A ASP* 2.7 30.3 + - - -
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Residues in contact with GLU 90 (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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86A ALA 3.1 17.5 + - - +
87A LEU* 3.6 10.3 - - + +
88A ILE 3.2 0.4 - - - -
89A ARG* 1.3 78.0 - - - +
91A LYS* 1.3 62.2 + - + +
92A HIS 5.1 0.2 - - - -
93A PRO* 5.2 2.4 - - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.5 19.3 + - - +
38A ASP* 2.5 39.4 + - - +
87A LEU* 3.3 23.5 + - - +
88A ILE* 3.2 8.3 + - - +
90A GLU* 1.3 80.6 - - + +
92A HIS* 1.3 80.3 + - + +
93A PRO* 3.9 7.5 - - - +
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Residues in contact with HIS 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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38A ASP* 2.7 32.1 + - + -
41A ILE* 3.5 42.4 - - + +
88A ILE* 3.0 28.4 + - + +
89A ARG* 2.8 38.2 + - - +
91A LYS* 1.3 95.2 + - + +
93A PRO* 1.3 55.7 - - - +
94A THR 3.5 2.6 + - - -
95A ILE* 3.4 21.6 - - + +
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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