Contacts of the helix formed by residues 77 - 89 (chain B) in PDB entry 6P1A
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 ASP 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 3.5 10.5 + - + +
76B ILE* 1.3 85.0 - - + +
78B LYS* 1.3 56.6 + - - +
79B LYS* 3.2 12.3 + - - +
80B ALA* 3.0 32.4 + - + +
81B PHE* 2.9 27.0 + - - +
133B ILE* 5.8 1.4 - - - +
140B MET* 6.4 2.7 - - + -
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Residues in contact with LYS 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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38B SER* 5.2 4.2 + - - -
39B VAL* 3.3 40.5 - - + +
74B MET 4.9 1.3 - - - +
75B TYR* 3.2 29.2 - - - +
76B ILE 3.6 4.8 + - - +
77B ASP* 1.3 73.1 + - - +
79B LYS* 1.3 57.7 + - - +
81B PHE* 3.6 4.6 - - + +
82B GLY* 2.9 25.5 + - - -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 3.2 8.6 + - - +
78B LYS* 1.3 79.2 - - - +
80B ALA* 1.3 59.1 + - - +
82B GLY* 3.2 2.3 + - - -
83B ILE* 3.0 44.8 + - + +
101B TYR* 2.9 53.3 + - + +
129B GLU* 5.9 3.4 - - - -
133B ILE* 4.7 13.5 - - + -
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Residues in contact with ALA 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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74B MET* 3.6 19.9 - - + +
77B ASP* 3.0 28.8 + - + +
79B LYS* 1.3 73.6 - - - +
81B PHE* 1.3 59.7 + - - +
83B ILE* 3.2 3.8 + - - +
84B LEU* 2.9 29.8 + - - +
133B ILE* 3.5 31.9 - - + +
134B LEU* 5.9 0.2 - - - +
137B SER* 4.0 3.5 + - - +
140B MET* 6.5 0.2 - - + -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 4.7 0.4 - + - -
37B SER* 4.1 1.1 - - - -
39B VAL* 3.7 31.9 - - + -
40B ILE* 3.6 27.8 - - + -
70B VAL* 3.9 25.8 - - + -
71B ASP* 3.9 21.5 - - - -
74B MET* 3.3 39.4 - - + +
75B TYR 4.3 1.3 - - - -
77B ASP 2.9 16.1 + - - +
78B LYS* 3.6 8.7 - - + +
80B ALA* 1.3 77.8 - - - +
82B GLY* 1.3 62.2 + - - +
84B LEU* 3.3 3.9 + - + +
85B LEU* 2.9 46.8 + - + +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 5.2 2.6 - - - +
43B PHE* 4.4 6.4 - - - -
78B LYS 2.9 14.9 + - - -
79B LYS* 3.2 3.3 + - - -
81B PHE* 1.3 76.5 - - - +
83B ILE* 1.3 57.9 + - - +
85B LEU* 3.3 9.8 + - - +
86B SER* 2.9 34.6 + - - -
101B TYR* 5.3 4.5 - - - -
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Residues in contact with ILE 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 LYS* 3.0 30.6 + - + +
80B ALA* 3.2 7.4 + - - +
82B GLY* 1.3 76.4 - - - +
84B LEU* 1.3 62.5 - - - +
86B SER* 3.2 7.7 + - - -
87B TYR* 2.9 22.9 + - - +
97B ILE* 3.9 23.6 - - + +
101B TYR* 4.1 26.7 - - + +
130B VAL* 4.6 12.6 - - + -
133B ILE* 3.8 37.7 - - + -
134B LEU* 3.9 26.0 - - + -
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Residues in contact with LEU 84 (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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20B LEU* 4.4 3.1 - - + -
23B TRP* 4.6 11.4 - - + -
70B VAL* 3.8 29.6 - - + -
74B MET* 4.3 11.2 - - + -
80B ALA 2.9 17.0 + - - +
81B PHE* 3.6 7.6 - - + +
83B ILE* 1.3 77.6 - - - +
85B LEU* 1.3 56.3 + - - +
87B TYR 3.3 0.3 + - - -
88B TYR* 2.9 62.4 + - + +
134B LEU* 4.2 14.6 - - + +
137B SER* 4.5 7.9 - - - -
138B LEU* 4.0 18.2 - - + -
141B ILE* 3.9 15.7 - - + -
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Residues in contact with LEU 85 (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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23B TRP* 3.5 33.9 - - + -
27B VAL* 4.9 2.7 - - + -
39B VAL* 4.4 5.6 - - + +
40B ILE* 4.1 21.8 - - + +
43B PHE* 3.7 45.3 - - + -
81B PHE* 2.9 42.5 + - + +
82B GLY* 3.8 2.7 - - - +
84B LEU* 1.3 74.6 - - - +
86B SER* 1.3 61.3 + - - +
89B ALA* 2.8 40.9 + - + +
90B HIS 2.9 8.7 + - - -
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Residues in contact with SER 86 (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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43B PHE* 3.8 11.2 - - - -
82B GLY 2.9 20.6 + - - -
83B ILE* 3.6 6.0 - - - -
85B LEU* 1.3 76.3 - - - +
87B TYR* 1.3 58.4 + - - +
90B HIS* 3.5 11.7 - - - +
91B GLY 3.1 8.0 + - - -
92B SER* 2.7 32.9 + - - -
97B ILE* 3.9 18.4 - - - -
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Residues in contact with TYR 87 (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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115A GLY 3.8 13.3 + - - -
117A ARG* 2.9 60.1 + - + +
17B ASN* 4.5 4.7 + - - -
21B GLU* 4.5 1.1 - - - +
83B ILE 2.9 17.0 + - - +
84B LEU 3.7 3.1 - - - +
85B LEU 3.1 0.2 - - - -
86B SER* 1.3 77.7 - - - +
88B TYR* 1.3 98.2 + + + +
91B GLY* 3.1 17.3 - - - -
92B SER 3.3 15.0 - - - -
93B SER 4.4 0.7 - - - -
94B LYS* 3.7 30.1 - - + +
97B ILE* 4.3 6.1 - - + -
134B LEU* 4.0 21.3 - - + -
201B EDO 3.8 22.3 - - - -
11E T 4.5 3.9 + - - -
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Residues in contact with TYR 88 (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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17B ASN* 2.8 36.4 + - - -
20B LEU* 3.6 45.8 - - + +
21B GLU* 3.6 27.9 - - - +
23B TRP* 4.5 7.0 - + + -
24B GLY* 3.7 12.0 - - - -
25B ALA 4.2 0.7 + - - -
55B ARG* 3.7 15.4 + - - -
84B LEU* 2.9 46.2 + - + +
87B TYR* 1.3 100.6 - + + +
89B ALA* 1.3 66.8 + - - +
134B LEU* 4.9 2.9 - - + -
138B LEU* 3.4 24.6 - - + +
201B EDO 3.9 5.9 + - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 5.5 0.2 - - + -
24B GLY* 3.4 24.5 - - - +
27B VAL* 4.6 9.4 - - + -
28B TYR* 3.3 16.2 - - + -
43B PHE* 4.2 14.1 - - + -
55B ARG* 2.7 28.1 + - - -
84B LEU 4.2 0.2 + - - -
85B LEU* 2.8 35.6 + - + +
88B TYR* 1.3 75.1 - - - +
90B HIS* 1.3 56.5 + - - +
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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