Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 6P7B
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 PRO 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.7 28.7 - - + +
66B SER* 1.3 82.2 - - - +
68B ASN* 1.3 68.9 + - - +
69B SER 3.1 1.6 - - - -
70B LYS* 3.1 38.0 + - + +
71B ILE* 3.7 6.2 + - - +
25E G 5.9 2.2 - - - -
26E T 6.2 4.0 - - + -
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Residues in contact with ASN 68 (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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8B ILE* 3.3 32.1 + - + +
9B GLY* 3.7 20.4 - - - -
10B ILE* 4.3 4.2 + - - +
62B GLN* 3.4 37.4 - - + +
66B SER* 3.2 7.4 - - - +
67B PRO* 1.3 83.4 - - - +
69B SER* 1.3 62.1 + - - +
71B ILE* 3.3 8.2 + - - +
72B ILE* 3.3 23.4 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 4.4 4.2 + - - -
63B GLY 4.5 7.4 - - - -
64B PHE 5.2 3.7 + - - -
66B SER* 2.8 23.9 + - - -
68B ASN* 1.3 78.8 - - - +
70B LYS* 1.3 63.2 + - - +
72B ILE* 3.1 18.9 + - - +
73B TYR* 3.3 27.3 - - - -
17F C 4.3 25.8 - - - +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.8 22.8 - - - +
41B TRP* 3.9 26.3 - - + +
67B PRO* 3.1 29.3 + - + +
69B SER* 1.3 84.9 + - - +
71B ILE* 1.3 66.7 + - + +
73B TYR* 3.8 2.1 + - - -
74B PHE* 3.4 19.6 + - - +
73D TYR* 3.7 59.9 + - + +
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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
----------------------------------------------------------
8B ILE* 3.7 25.4 - - + -
9B GLY 5.7 0.4 - - - +
10B ILE* 5.1 12.3 - - + +
37B TRP* 4.0 18.8 - - + -
41B TRP* 3.4 39.7 - - + -
45B VAL* 4.1 10.8 - - + -
67B PRO 3.9 11.0 - - - +
68B ASN* 3.6 7.6 - - - +
69B SER 3.2 0.8 - - - -
70B LYS* 1.3 84.6 - - + +
72B ILE* 1.3 67.2 + - - +
74B PHE* 3.3 4.4 + - - +
75B ILE* 2.9 42.5 + - + +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.9 4.9 - - + -
59B LEU* 3.6 39.5 - - + +
60B GLU 4.3 3.4 - - - +
61B LYS* 5.3 0.2 - - - -
62B GLN* 3.7 21.8 - - - +
68B ASN 3.3 15.0 + - - +
69B SER* 3.1 12.3 + - - +
71B ILE* 1.3 78.3 - - - +
73B TYR* 1.3 71.6 + - + +
75B ILE* 3.2 3.3 + - - +
76B LYS* 2.9 37.0 + - + +
88B VAL* 4.1 31.6 - - + -
17F C 6.1 4.0 - - - +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 3.3 33.1 + - - +
70B LYS* 3.8 4.7 + - - +
71B ILE 3.3 0.2 - - - -
72B ILE* 1.3 81.3 - - + +
74B PHE* 1.3 60.2 + - - +
76B LYS* 3.7 25.0 - - + +
77B GLY 2.9 24.3 + - - -
41D TRP* 3.9 34.3 - + - -
70D LYS* 3.8 38.1 - - + +
73D TYR* 4.5 2.7 - + + -
74D PHE* 3.6 18.7 - + + +
16F T 5.0 4.0 - - + +
17F C 3.0 52.5 + + + -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TRP* 3.6 27.6 - + + -
42B GLU* 3.5 42.2 - - + -
45B VAL* 3.9 26.5 - - + -
46B ALA* 4.8 1.8 - - + -
70B LYS 3.4 13.2 + - - +
71B ILE 3.3 7.8 + - - +
73B TYR* 1.3 79.3 - - - +
75B ILE* 1.3 58.6 + - + +
77B GLY 3.4 0.3 + - - -
78B PHE* 2.9 41.8 + + + +
73D TYR* 3.7 14.6 + - + +
76D LYS* 4.1 11.2 - - + -
77D GLY* 3.4 31.4 - - - -
80D TYR* 4.1 20.2 - + + -
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.2 6.3 - - + -
37B TRP* 5.3 2.7 - - + -
45B VAL* 3.8 14.6 - - + -
49B LEU* 3.6 29.4 - - + -
57B VAL* 4.4 4.0 - - + -
59B LEU* 4.1 27.1 - - + -
71B ILE* 2.9 36.9 + - + +
72B ILE 3.6 3.8 - - - +
74B PHE* 1.3 75.5 - - + +
76B LYS* 1.3 63.0 + - - +
78B PHE* 3.1 6.5 + - - +
79B PHE* 2.9 44.0 + - + +
86B VAL* 4.2 17.9 - - + +
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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 ILE* 2.9 30.8 + - + +
73B TYR* 3.7 28.9 - - + +
75B ILE* 1.3 76.9 - - - +
77B GLY* 1.3 61.6 + - - +
79B PHE 3.8 1.0 - - - -
80B TYR* 3.0 27.2 + - - +
85B LYS* 6.1 2.4 - - - +
86B VAL* 3.7 42.6 + - + +
88B VAL* 4.5 10.7 - - + +
41D TRP* 5.6 1.8 - - - -
42D GLU* 3.3 32.9 + - - +
74D PHE* 3.9 9.3 - - + -
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Residues in contact with GLY 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 TYR 2.9 12.6 + - - -
74B PHE 3.9 0.7 - - - -
76B LYS* 1.3 77.4 - - - +
78B PHE* 1.3 63.0 + - - +
80B TYR 3.4 7.4 + - - +
74D PHE* 3.4 39.4 - - - -
78D PHE* 3.2 29.8 - - - -
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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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45B VAL* 6.3 0.9 - - + -
46B ALA* 3.8 32.5 - - + -
49B LEU* 5.6 2.0 - - + -
50B THR* 3.5 30.1 - - + -
74B PHE* 2.9 27.8 + + + +
75B ILE* 3.1 8.0 + - - +
77B GLY* 1.3 78.3 - - - +
79B PHE* 1.3 85.3 + + - +
80B TYR 3.4 4.3 + - - +
82B SER* 5.0 1.0 + - - -
77D GLY* 3.3 19.7 + - - +
78D PHE* 4.6 2.0 - - - +
80D TYR* 4.3 15.7 - + + -
81D ASN* 3.8 31.4 + - + -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.6 54.3 - - + -
50B THR* 4.4 7.0 - - + -
54B PRO* 4.9 4.5 - - + -
57B VAL* 3.8 20.0 - - + -
75B ILE* 2.9 31.5 + - + +
76B LYS 3.8 1.3 - - - -
78B PHE* 1.3 94.8 - + - +
80B TYR* 1.3 62.4 + - - +
82B SER* 2.2 32.2 + - - +
84B THR* 3.5 45.0 - - + +
86B VAL* 4.1 11.6 - - + +
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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