Contacts of the helix formed by residues 68 - 83 (chain B) in PDB entry 2H1H
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 SER 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ALA* 2.9 33.6 + - - +
66B TRP 3.5 0.2 - - - -
67B PHE* 1.3 78.4 - - - +
69B ALA* 1.3 54.5 + - - +
70B PRO* 3.5 11.0 - - - +
71B ILE* 3.4 16.1 + - - +
72B LYS* 2.5 39.2 + - - +
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Residues in contact with ALA 69 (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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68B SER* 1.3 72.6 - - - +
70B PRO* 1.3 68.5 - - + +
72B LYS* 3.6 4.2 - - - +
73B ALA* 3.0 29.2 + - - +
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Residues in contact with PRO 70 (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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68B SER* 3.5 11.9 - - - +
69B ALA* 1.3 91.8 - - + +
71B ILE* 1.3 68.2 + - + +
73B ALA* 2.7 26.8 + - + +
74B GLU* 2.8 24.8 + - + +
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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
----------------------------------------------------------
61B ARG* 3.8 21.5 - - - +
62B TRP* 3.3 48.9 - - + +
64B LYS* 5.3 2.7 - - + -
65B ALA* 3.4 22.2 - - + +
66B TRP* 3.2 29.4 - - - +
68B SER* 3.4 9.1 + - - +
70B PRO* 1.3 83.1 - - + +
72B LYS* 1.3 62.0 + - - +
74B GLU* 3.3 8.4 + - - +
75B ARG* 3.0 31.4 + - - +
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Residues in contact with LYS 72 (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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66B TRP 3.6 9.1 + - - +
67B PHE* 3.1 40.4 + - - +
68B SER 2.5 16.8 + - - +
69B ALA* 3.6 5.4 - - - +
70B PRO 3.1 0.4 - - - -
71B ILE* 1.3 79.8 - - - +
73B ALA* 1.3 61.0 + - - +
75B ARG* 3.8 21.1 + - - +
76B LYS* 3.4 19.9 + - - +
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Residues in contact with ALA 73 (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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69B ALA 3.0 13.7 + - - +
70B PRO* 2.7 14.7 + - + +
72B LYS* 1.3 75.5 - - - +
74B GLU* 1.3 62.3 + - + -
75B ARG 3.2 2.0 - - - -
76B LYS* 3.3 10.5 + - + +
77B ALA* 3.0 21.8 + - - +
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Residues in contact with GLU 74 (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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61B ARG* 2.7 40.6 + - - -
62B TRP* 2.7 31.5 + - + +
70B PRO* 2.8 31.6 + - + +
71B ILE* 3.9 8.3 - - - +
73B ALA* 1.3 72.7 - - + +
75B ARG* 1.3 54.1 + - - +
77B ALA* 3.0 8.7 + - - +
78B PHE* 2.7 35.9 + - - +
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Residues in contact with ARG 75 (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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62B TRP* 3.7 30.3 - - + -
66B TRP* 2.6 82.8 + - - +
67B PHE* 4.2 9.5 - - - -
71B ILE* 3.0 16.4 + - - +
72B LYS* 3.8 22.1 + - - +
74B GLU* 1.3 76.7 - - - +
76B LYS* 1.3 63.9 + - - +
78B PHE* 3.2 7.7 + - + +
79B ARG* 2.6 79.6 + - - +
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Residues in contact with LYS 76 (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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72B LYS 3.4 11.5 + - - +
73B ALA* 3.3 14.1 + - + +
75B ARG* 1.3 78.6 - - - +
77B ALA* 1.3 66.1 + - + +
79B ARG* 3.3 13.8 + - - +
80B GLU* 2.9 49.6 + - + +
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Residues in contact with ALA 77 (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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73B ALA 3.0 13.2 + - - +
74B GLU* 3.4 11.2 - - - +
76B LYS* 1.3 78.4 - - + +
78B PHE* 1.3 66.9 + - - +
80B GLU* 3.1 13.1 + - - +
81B ALA* 3.0 21.9 + - - +
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Residues in contact with PHE 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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36B VAL* 4.2 16.4 - - + -
55B ILE* 3.8 22.9 - - + -
56B PRO 3.7 21.3 - - - +
57B VAL* 4.2 9.2 - - + -
62B TRP* 3.8 29.4 - + + -
74B GLU 2.7 19.0 + - - +
75B ARG* 3.2 4.5 + - - +
77B ALA* 1.3 72.8 - - - +
79B ARG* 1.3 65.2 + - + +
81B ALA* 3.0 8.7 + - + +
82B LEU* 2.6 58.0 + - + +
102B LEU* 3.9 20.9 - - + -
103B VAL* 4.2 15.9 - - + -
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Residues in contact with ARG 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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66B TRP* 4.5 6.1 - - - -
75B ARG* 2.6 72.0 + - - +
76B LYS* 3.5 9.8 - - - +
78B PHE* 1.3 88.4 - - + +
80B GLU* 1.3 59.4 + - + +
82B LEU* 4.1 5.6 - - - -
83B GLN* 2.9 42.8 + - - +
102B LEU* 4.9 11.9 + - - +
106B LEU* 3.9 31.2 - - + +
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Residues in contact with GLU 80 (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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76B LYS* 2.9 44.5 + - + +
77B ALA* 3.1 11.4 + - - +
79B ARG* 1.3 75.4 - - + +
81B ALA* 1.3 62.1 + - - +
83B GLN* 3.5 8.5 + - - +
84B ALA* 3.2 22.2 + - - +
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Residues in contact with ALA 81 (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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53B ARG* 6.1 2.9 - - - +
55B ILE* 3.9 25.0 - - + +
77B ALA 3.0 12.6 + - - +
78B PHE* 3.3 11.4 - - + +
80B GLU* 1.3 75.5 - - - +
82B LEU* 1.3 65.4 + - - +
84B ALA* 3.4 18.8 + - - +
87B TYR* 5.5 0.2 + - - -
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Residues in contact with LEU 82 (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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4B LEU* 3.6 29.6 - - + +
36B VAL* 3.9 20.2 - - + -
55B ILE* 4.3 7.9 - - + +
78B PHE* 2.6 45.9 + - + +
79B ARG* 3.5 8.7 - - - +
81B ALA* 1.3 75.0 - - - +
83B GLN* 1.3 58.6 + - + +
84B ALA 3.3 3.6 + - - -
85B LYS 4.4 1.0 + - - +
87B TYR* 4.2 18.5 + - - -
102B LEU 4.4 0.4 - - - +
103B VAL* 3.4 29.2 - - + +
106B LEU* 4.0 17.5 - - + -
107B ALA* 4.1 12.3 - - + +
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Residues in contact with GLN 83 (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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79B ARG* 2.9 28.2 + - - +
80B GLU* 3.6 7.8 - - - +
82B LEU* 1.3 76.1 - - + +
84B ALA* 1.3 62.2 + - - +
85B LYS 3.2 3.8 - - - -
106B LEU* 2.9 45.9 - - + +
107B ALA* 4.7 0.2 - - - -
108B HIS* 3.2 44.0 + - + +
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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