Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 2R5N
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 GLY 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B HIS 4.4 1.1 - - - -
29B ALA* 4.4 6.7 - - - -
30B PRO* 3.6 26.2 - - - -
62B LEU* 3.4 11.2 - - - +
64B ASN 3.1 10.4 + - - -
65B GLY 3.0 2.0 - - - -
66B HIS* 1.3 77.1 - - - +
68B SER* 1.3 56.6 - - - -
69B MET 3.2 3.6 - - - -
70B LEU* 2.9 31.7 + - - +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.1 7.0 - - - -
65B GLY 3.2 11.1 + - - -
66B HIS 2.8 8.9 + - - -
67B GLY* 1.3 72.1 - - - +
69B MET* 1.3 64.3 + - - +
71B ILE* 3.1 8.1 + - - +
72B TYR* 3.0 39.8 + - - -
90B PHE* 3.3 17.2 - - - -
99B GLY 2.7 28.4 + - - -
101B PRO* 3.9 13.9 - - - -
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Residues in contact with MET 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.7 10.3 - - - +
15B SER* 3.5 26.9 - - - +
18B ALA* 3.5 32.3 - - + -
19B VAL* 4.3 4.5 - - + -
26B HIS 5.3 1.1 + - - +
30B PRO* 4.5 4.7 - - + +
67B GLY 3.2 1.4 + - - -
68B SER* 1.3 82.1 + - - +
70B LEU* 1.3 56.0 + - - +
72B TYR* 3.9 12.1 - - + -
73B SER* 2.8 47.9 + - - +
87B LEU* 4.0 24.9 - - + -
90B PHE* 3.8 41.9 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.6 25.8 - - + -
15B SER* 4.3 1.6 - - - -
29B ALA* 4.8 1.8 - - + +
30B PRO* 3.8 28.0 - - + +
33B MET* 3.9 19.3 - - + -
34B ALA* 4.5 2.2 - - - -
37B ALA* 3.8 21.3 - - + -
60B PHE* 5.8 0.4 - - + -
62B LEU* 4.0 12.8 - - + -
67B GLY* 2.9 16.1 + - - +
69B MET* 1.3 78.2 - - - +
71B ILE* 1.3 63.0 + - - +
73B SER* 3.4 2.4 + - - -
74B LEU* 3.1 35.0 + - + +
152B PHE* 3.8 29.6 - - + -
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 4.8 6.3 - - + -
60B PHE* 4.0 33.9 - - + +
62B LEU* 4.1 18.1 - - + +
67B GLY 3.9 0.6 + - - -
68B SER 3.1 13.6 + - - +
70B LEU* 1.3 76.4 - - + +
72B TYR* 1.3 71.1 + - + +
74B LEU* 3.2 6.9 + - - +
75B LEU* 2.9 48.7 + - + +
101B PRO* 3.9 27.1 - - + -
108B GLY 4.7 4.5 - - - +
109B VAL* 4.3 26.2 - - + -
110B GLU* 5.4 1.3 - - + +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 3.0 32.5 + - - +
69B MET* 3.9 24.9 - - + +
71B ILE* 1.3 87.3 - - + +
73B SER* 1.3 56.9 + - - +
75B LEU* 3.4 2.0 + - + -
76B HIS* 2.9 31.4 + - - +
82B LEU* 3.7 26.2 - - + +
87B LEU* 4.2 8.0 - - + +
90B PHE* 3.8 3.6 - + - -
96B LYS 4.1 10.8 - - - -
97B THR* 3.6 27.6 - - + -
98B PRO* 2.6 46.6 + - - +
101B PRO* 3.4 14.1 - - + +
102B GLU 4.6 0.2 + - - -
106B THR* 4.1 12.3 - - + -
109B VAL* 4.5 7.2 - - + -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.8 26.4 + - - -
14B LEU* 3.4 29.5 - - - +
15B SER* 3.4 11.4 + - - -
69B MET* 2.8 28.8 + - - +
70B LEU 3.6 3.8 - - - -
72B TYR* 1.3 76.7 - - - +
74B LEU* 1.3 56.8 + - - +
76B HIS* 3.8 0.3 - - - +
77B LEU* 2.8 38.2 + - - +
87B LEU* 4.6 3.8 - - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.7 14.6 - - + -
37B ALA* 4.0 18.2 - - + -
41B TRP* 3.7 50.5 - - + +
60B PHE* 4.9 6.5 - - + -
70B LEU* 3.1 29.6 + - + +
71B ILE* 3.2 9.6 + - - +
73B SER* 1.3 74.9 - - - +
75B LEU* 1.3 61.1 + - - +
77B LEU* 4.7 2.7 - - - -
78B THR* 2.9 34.8 + - - +
294B TRP* 3.7 34.5 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 4.0 14.1 - - + -
71B ILE* 2.9 36.7 + - + +
72B TYR* 4.0 3.8 - - + +
74B LEU* 1.3 71.3 - - - +
76B HIS* 1.3 63.0 + - - +
79B GLY 3.4 3.8 + - - -
80B TYR* 3.0 61.1 + - + +
82B LEU* 4.0 11.7 - - + -
106B THR* 4.2 8.3 - - + -
107B ALA 3.4 25.8 - - - +
108B GLY* 3.8 15.5 - - - +
109B VAL* 3.8 24.5 - - + -
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Residues in contact with HIS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.5 9.2 - - + -
72B TYR 2.9 18.9 + - - +
73B SER 3.8 2.0 - - - +
75B LEU* 1.3 78.2 - - - +
77B LEU* 1.3 65.3 + - + +
79B GLY* 3.2 13.7 + - - -
80B TYR 4.8 2.6 - - - +
82B LEU* 2.8 31.1 + - - +
83B PRO* 3.7 2.9 - - + -
84B MET* 3.4 41.1 + - + +
87B LEU* 3.9 18.8 - - + -
291B TYR* 2.6 42.3 + + - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA* 4.2 10.3 - - + -
11B ILE* 4.0 20.4 - - + -
14B LEU* 4.1 21.5 - - + -
73B SER 2.8 26.4 + - - +
74B LEU 4.1 1.8 - - - +
76B HIS* 1.3 75.6 - - + +
78B THR* 1.3 60.5 + - - +
79B GLY 3.3 0.9 + - - -
286B ILE* 4.1 28.3 - - + -
290B ILE* 4.7 0.4 - - + -
291B TYR* 4.2 22.9 - - + -
294B TRP* 3.4 61.3 - - + +
295B ASP* 3.6 9.2 + - - +
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Residues in contact with THR 78 (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 TRP* 3.9 21.5 - - + +
42B ARG* 5.9 0.7 - - + -
47B HIS* 3.9 13.9 - - + +
49B PRO* 3.3 11.5 - - - +
74B LEU 2.9 24.4 + - - +
77B LEU* 1.3 75.4 - - - +
79B GLY* 1.3 57.2 + - - +
80B TYR* 3.2 24.6 - - - -
294B TRP* 3.5 39.7 - - + +
295B ASP* 3.6 2.6 - - - +
296B ALA* 2.8 26.5 + - + -
297B LYS 4.0 0.5 + - - -
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Residues in contact with GLY 79 (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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49B PRO* 3.6 12.8 - - - +
50B GLN* 5.9 0.2 - - - +
76B HIS 3.2 12.0 + - - -
77B LEU 3.3 1.2 - - - -
78B THR* 1.3 79.3 - - - +
80B TYR* 1.3 67.7 + - - +
295B ASP* 3.5 15.0 - - - -
297B LYS* 3.4 24.5 - - - +
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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