Contacts of the helix formed by residues 86 - 101 (chain B) 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 HIS 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 4.1 12.7 + - + +
81B LEU* 3.9 9.2 - - - -
85B ALA* 1.3 70.5 - - - +
87B LYS* 1.3 79.3 + - + +
88B THR 3.1 0.4 - - - -
89B ASN* 2.9 16.4 + - - +
205B GLN* 2.9 31.4 + - - -
208B ILE* 4.0 20.9 - - + -
235B SER* 3.0 21.5 + - - -
236B ASN* 3.2 31.1 - - + +
377B SER* 3.0 22.2 + - - +
399B PLP 3.0 45.5 + + - -
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 3.1 9.1 - - + -
86B HIS* 1.3 90.9 + - + +
88B THR* 1.3 63.4 + - - +
89B ASN 3.2 0.7 + - - -
90B GLN* 3.3 18.9 + - + +
91B VAL* 3.3 16.8 + - + +
114B GLN* 3.8 20.0 - - + -
115B HIS* 3.7 38.1 - - + +
118B ALA* 4.2 12.6 - - + -
189B GLY 4.9 13.4 + - - +
205B GLN* 4.0 6.1 - - - +
235B SER* 5.6 0.6 + - - +
399B PLP 1.6 64.0 + - - +
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 5.3 0.7 - - + -
53B ALA* 4.5 12.3 - - + -
81B LEU* 3.9 9.9 - - - -
82B HIS* 2.6 33.1 + - + +
83B GLY* 4.2 5.4 - - - -
85B ALA 3.6 4.3 + - - -
86B HIS 3.0 0.4 + - - -
87B LYS* 1.3 78.9 - - - +
89B ASN* 1.3 64.2 + - - +
91B VAL* 2.9 23.4 - - + +
92B LEU* 3.1 30.8 + - + +
118B ALA* 4.6 4.1 - - - +
121B LEU* 4.3 22.8 - - + +
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.5 15.4 - - - -
49B LEU* 3.5 22.6 - - + +
53B ALA* 5.1 0.2 - - - +
55B ARG* 3.0 34.6 + - - +
78B GLU* 3.3 10.3 + - - -
81B LEU* 3.3 11.0 - - - +
86B HIS 2.9 12.2 + - - +
88B THR* 1.3 80.4 - - - +
90B GLN* 1.3 60.6 + - - +
92B LEU* 3.8 0.7 - - - +
93B GLY 3.4 14.0 + - - -
204B PHE 3.5 11.4 - - - +
205B GLN* 3.1 25.2 + - - +
207B MET* 4.1 10.0 - - - -
208B ILE* 4.0 6.3 - - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.3 13.0 + - + +
89B ASN* 1.3 77.7 - - - +
91B VAL* 1.3 76.2 + - - +
92B LEU 3.3 0.2 - - - -
93B GLY* 3.9 0.3 - - - -
94B GLN* 2.6 52.5 + - - +
115B HIS* 4.1 1.6 + - - -
188B LEU 2.9 22.8 + - - -
189B GLY* 3.6 19.7 + - - +
201B VAL* 3.5 23.8 - - + +
204B PHE* 3.9 18.9 - - + -
205B GLN* 3.5 26.0 - - + +
235B SER* 5.8 1.3 - - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS 3.6 7.9 - - - +
88B THR* 2.9 36.8 - - + +
90B GLN* 1.3 89.8 - - - +
92B LEU* 1.3 61.3 + - + +
94B GLN* 4.5 0.2 - - - -
95B ALA* 2.9 31.2 + - - +
115B HIS* 4.0 16.8 - - + -
118B ALA* 3.7 30.5 - - + +
119B SER* 4.1 2.0 - - - +
121B LEU* 5.3 0.2 - - + -
122B ALA* 4.1 8.2 - - + +
187B MET* 3.4 29.9 - - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 4.1 10.5 - - + -
48B LEU* 4.2 30.3 - - + -
49B LEU* 4.2 13.2 - - + -
52B TYR* 4.3 14.6 - - + -
53B ALA* 4.1 17.7 - - + -
88B THR* 3.1 38.2 + - + +
89B ASN 3.8 3.6 - - - +
91B VAL* 1.3 77.7 - - + +
93B GLY* 1.3 61.4 + - - +
95B ALA* 3.2 6.1 + - - +
96B LEU* 3.0 26.7 + - - +
121B LEU* 5.1 0.4 - - + -
122B ALA* 4.4 15.0 - - + -
125B LEU* 4.3 18.8 - - + -
126B LEU* 4.3 4.0 - - + +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.9 2.7 - - - -
45B PHE* 3.4 27.0 - - - -
89B ASN 3.4 3.8 + - - -
90B GLN 3.5 0.4 + - - -
91B VAL 3.3 0.2 - - - -
92B LEU* 1.3 80.3 - - - +
94B GLN* 1.3 60.1 + - - +
96B LEU* 3.1 7.6 + - - +
97B LEU* 3.0 18.0 + - - +
204B PHE* 3.4 28.5 - - - -
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLN* 2.6 43.7 + - - +
93B GLY* 1.3 75.0 - - - +
95B ALA* 1.3 57.1 + - - +
97B LEU* 3.3 7.5 + - + +
98B ALA* 3.0 28.2 + - - +
185B HIS* 2.8 33.0 + - - +
186B TYR 3.5 2.6 - - - +
187B MET* 3.5 29.1 - - + +
188B LEU* 2.9 23.2 + - - +
197B TYR* 3.5 12.9 - - - -
200B ILE* 4.5 9.2 - - + -
201B VAL* 4.2 7.5 - - - +
204B PHE* 3.6 14.5 - - + -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL 2.9 19.4 + - - +
92B LEU* 3.3 4.7 - - - +
93B GLY 3.1 0.2 - - - -
94B GLN* 1.3 78.2 - - - +
96B LEU* 1.3 60.6 + - - +
98B ALA* 3.4 6.4 + - - +
99B LYS* 3.2 26.3 + - - +
122B ALA* 4.3 9.9 - - + -
126B LEU* 3.3 25.1 - - + -
128B LEU* 3.9 14.0 - - + +
187B MET* 3.6 13.4 - - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.6 16.9 - - + -
44B GLN* 3.3 38.8 - - + +
45B PHE* 3.6 45.1 - - + +
48B LEU* 3.8 22.4 - - + -
92B LEU 3.0 15.9 + - - +
93B GLY 3.1 7.2 + - - +
95B ALA* 1.3 75.4 - - - +
97B LEU* 1.3 58.9 + - - +
99B LYS* 3.3 11.0 + - + +
100B ARG* 2.9 27.9 + - - +
126B LEU* 4.3 12.8 - - + -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.3 20.2 - - + +
31B ALA* 3.8 37.5 - - + +
32B PHE* 3.8 22.0 - - + +
35B ALA* 3.9 12.3 - - + -
41B PHE* 4.0 5.1 - - + -
93B GLY 3.0 7.6 + - - +
94B GLN* 3.5 12.6 - - + +
96B LEU* 1.3 74.0 - - - +
98B ALA* 1.3 67.4 + - - +
100B ARG* 3.2 7.9 + - - +
101B MET* 3.0 31.2 + - + +
185B HIS* 5.6 1.1 - - + +
200B ILE* 4.3 6.5 - - + -
204B PHE* 3.8 34.3 - - + -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLN 3.0 11.6 + - - +
95B ALA 3.6 9.4 - - - +
96B LEU 3.3 0.2 - - - -
97B LEU* 1.3 78.3 - - - +
99B LYS* 1.3 60.6 + - - +
101B MET* 3.1 19.2 + - - +
103B LYS* 2.9 35.4 + - + +
105B GLU 5.2 0.4 - - - +
106B ILE* 3.9 14.8 - - + -
128B LEU* 4.8 3.6 - - + -
185B HIS* 3.6 27.1 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 5.7 4.7 - - - -
95B ALA 3.2 13.6 + - - +
96B LEU* 3.7 12.1 - - + +
97B LEU 3.2 0.4 - - - -
98B ALA* 1.3 72.8 - - - +
100B ARG* 1.3 62.0 + - - +
102B GLY* 2.9 20.3 + - - -
103B LYS 4.0 7.6 - - - +
126B LEU* 2.9 54.2 + - + +
127B GLY 4.6 4.2 + - - -
128B LEU* 4.0 17.9 - - + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 3.7 14.2 + - + +
34B SER* 2.7 35.6 + - - -
35B ALA* 3.5 35.5 - - - +
38B ASP* 3.1 31.3 + - - +
41B PHE* 4.2 14.0 - - + +
96B LEU 2.9 15.5 + - - +
97B LEU* 3.2 15.9 + - - +
99B LYS* 1.3 77.1 - - - +
101B MET* 1.3 59.3 + - + +
102B GLY 3.2 1.1 + - - -
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLN* 3.9 34.7 + - + +
28B LEU* 3.9 20.4 - - + -
31B ALA* 3.5 31.9 - - + -
97B LEU* 3.0 21.1 + - + +
98B ALA* 3.6 10.1 - - - +
99B LYS 3.1 0.8 - - - -
100B ARG* 1.3 76.2 - - - +
102B GLY* 1.3 62.0 + - - +
103B LYS* 3.3 36.1 + - + +
182B GLU 5.3 1.6 - - - +
185B HIS* 3.7 22.7 - - - +
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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
------------------------------------------------------------
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