Contacts of the helix formed by residues 69 - 84 (chain B) in PDB entry 3P9K
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 GLU 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A GLY* 5.6 0.2 - - - -
148A GLY 5.3 4.5 + - - +
67B ASN* 2.8 14.1 + - - +
68B PRO* 1.3 82.9 - - + +
70B ALA* 1.3 65.2 + - - +
71B PRO* 3.3 3.8 - - - -
72B ASP* 2.9 25.1 + - + +
73B MET* 3.0 34.0 + - + +
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Residues in contact with ALA 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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144A VAL* 3.8 17.0 - - + +
59B ALA* 4.2 8.1 - - + -
62B LEU* 5.7 0.7 - - + -
64B SER* 3.6 22.9 - - - +
67B ASN* 3.3 25.3 + - - +
69B GLU* 1.3 76.5 - - - +
71B PRO* 1.3 64.8 - - + +
73B MET* 3.2 4.9 + - - +
74B VAL* 2.8 35.3 + - + +
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Residues in contact with PRO 71 (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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55B PRO* 3.2 24.1 - - + +
56B THR* 3.9 35.4 - - + +
59B ALA* 4.0 13.2 - - + -
67B ASN 4.6 0.4 - - - +
68B PRO 3.5 14.4 - - - +
69B GLU* 3.3 5.4 - - - -
70B ALA* 1.3 95.2 - - + +
72B ASP* 1.3 56.9 + - - +
74B VAL* 3.4 1.0 + - + +
75B ASP* 2.9 25.0 + - - +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 2.8 43.3 + - - -
69B GLU* 2.9 20.2 + - + +
71B PRO* 1.3 78.3 - - - +
73B MET* 1.3 66.0 + - - +
75B ASP* 3.2 11.3 + - - +
76B ARG* 3.1 36.6 + - - +
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Residues in contact with MET 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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140A LEU* 5.7 0.7 - - - -
143A ALA* 3.6 18.6 - - + +
144A VAL* 3.8 22.7 - - + -
147A GLY* 4.8 1.6 - - - -
148A GLY 3.9 22.0 - - - +
318A LEU* 4.2 32.2 - - + +
67B ASN* 3.5 22.9 - - - +
69B GLU* 3.0 33.3 + - + +
70B ALA* 3.6 5.6 - - - +
72B ASP* 1.3 78.9 - - + +
74B VAL* 1.3 62.2 + - - +
76B ARG* 3.2 11.9 + - - +
77B ILE* 3.0 29.6 + - - +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 4.4 11.0 - - + -
41B LEU* 4.4 10.3 - - + -
55B PRO* 4.1 10.1 - - + +
58B VAL* 3.8 29.8 - - + -
59B ALA* 4.4 6.7 - - + -
62B LEU* 4.2 24.9 - - + -
70B ALA 2.8 24.2 + - - +
71B PRO 3.6 4.7 - - - +
73B MET* 1.3 75.4 - - - +
75B ASP* 1.3 58.5 + - - +
77B ILE* 3.3 8.6 + - + +
78B LEU* 2.9 43.1 + - + +
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Residues in contact with ASP 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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55B PRO* 3.5 22.9 - - + +
71B PRO 2.9 18.2 + - - +
72B ASP* 3.3 11.6 - - - +
74B VAL* 1.3 77.7 - - - +
76B ARG* 1.3 58.5 + - + +
78B LEU 3.3 1.0 + - - -
79B ARG* 2.8 29.2 + - - +
101B ARG* 2.8 36.7 + - - +
103B TYR* 2.5 38.3 + - - -
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Residues in contact with ARG 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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311A PHE* 5.9 0.2 - - - +
314A ASP* 2.9 63.8 + - - +
315A MET* 3.8 12.3 - - - +
318A LEU* 3.6 29.7 - - + +
323A GLY 4.9 2.6 + - - -
324A GLY 3.0 27.1 + - - -
325A ARG* 3.4 30.4 - - - +
72B ASP* 3.1 31.7 + - - +
73B MET* 3.2 9.6 + - - +
75B ASP* 1.3 76.8 - - + +
77B ILE* 1.3 63.6 + - - +
79B ARG* 3.4 17.1 + - - +
80B LEU* 3.2 22.9 + - - +
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Residues in contact with ILE 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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140A LEU* 4.3 15.9 - - + -
144A VAL* 4.1 26.7 - - + -
315A MET* 3.9 25.6 - - + -
318A LEU* 4.5 2.7 - - + -
32B THR* 3.8 17.3 - - + +
35B ASN* 5.6 1.3 - - + -
36B ALA* 4.3 4.9 - - + +
39B LEU* 4.5 12.3 - - + -
41B LEU* 3.8 20.9 - - + -
73B MET 3.0 21.0 + - - +
74B VAL* 3.5 10.3 - - - +
76B ARG* 1.3 77.2 - - - +
78B LEU* 1.3 58.6 + - - +
80B LEU* 3.3 5.4 + - - +
81B LEU* 3.1 36.1 + - + +
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Residues in contact with LEU 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 LEU* 4.1 21.3 - - + -
42B LEU* 5.4 0.7 - - + -
45B LEU* 4.4 21.8 - - + -
58B VAL* 4.5 16.8 - - + -
74B VAL* 2.9 37.8 + - + +
77B ILE* 1.3 73.9 - - - +
79B ARG* 1.3 61.2 + - - +
81B LEU* 3.7 20.1 - - + -
82B ALA* 2.8 31.0 + - - +
87B VAL* 3.8 8.8 - - + +
103B TYR* 3.7 45.0 - - + -
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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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297A LEU* 3.5 25.8 - - - +
311A PHE* 3.6 36.1 - - + +
314A ASP* 2.7 38.0 + - - -
325A ARG* 5.5 5.1 - - - +
328A TYR* 3.1 31.8 + - - -
75B ASP* 2.8 19.4 + - - +
76B ARG* 3.7 19.2 + - - +
77B ILE 3.3 0.2 - - - -
78B LEU* 1.3 76.9 - - - +
80B LEU* 1.3 63.9 + - - +
82B ALA* 3.4 4.3 + - - +
83B SER* 3.2 20.8 + - - -
89B CYS* 5.7 3.1 - - - -
101B ARG* 4.0 22.9 - - - +
103B TYR* 3.5 16.3 + - + +
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Residues in contact with LEU 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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311A PHE* 3.8 24.8 - - + +
312A HIS* 3.7 29.4 - - + -
315A MET* 3.9 21.8 - - + -
28B VAL* 4.0 7.9 - - + -
29B LEU* 4.3 15.3 - - + -
32B THR* 3.9 24.9 - - + +
76B ARG 3.2 10.4 + - - +
77B ILE 3.5 7.4 - - - +
79B ARG* 1.3 79.7 - - - +
81B LEU* 1.3 75.0 + - + +
83B SER* 2.6 29.3 + - - +
84B TYR* 3.6 7.6 + - + -
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Residues in contact with LEU 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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29B LEU* 4.1 13.7 - - + -
32B THR* 4.2 1.6 - - + -
33B LEU* 4.1 27.4 - - + +
36B ALA* 3.7 28.0 - - + -
42B LEU* 4.8 11.0 - - + -
77B ILE* 3.1 23.2 + - + +
78B LEU* 3.3 17.5 + - + +
80B LEU* 1.3 90.5 - - + +
82B ALA* 1.3 57.2 + - - +
84B TYR* 2.9 18.6 + - - +
86B VAL* 3.1 38.0 + - + +
87B VAL* 4.2 7.9 - - + -
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Residues in contact with ALA 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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303A ALA* 5.3 0.7 - - - +
78B LEU 2.8 18.0 + - - +
79B ARG* 3.5 6.7 - - - +
80B LEU 3.2 0.2 - - - -
81B LEU* 1.3 71.8 - - - +
83B SER* 1.3 58.8 + - - +
84B TYR 3.0 5.4 - - - -
85B ASN* 2.9 25.1 + - - -
87B VAL* 3.4 26.1 - - + +
89B CYS* 3.6 29.8 - - + +
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Residues in contact with SER 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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303A ALA* 3.5 22.9 - - - +
307A SER* 4.7 3.1 - - - -
308A GLN* 2.9 39.2 + - - +
311A PHE* 3.5 34.9 - - - -
79B ARG 3.2 2.6 + - - -
80B LEU* 2.6 22.9 + - - +
82B ALA* 1.3 77.4 - - - +
84B TYR* 1.3 61.5 + - - +
85B ASN* 3.4 0.8 - - - -
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Residues in contact with TYR 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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19A PHE* 3.5 18.6 - - + -
23A LEU* 5.8 0.2 - - + -
308A GLN* 3.0 30.3 - - + +
312A HIS* 2.5 41.8 + + - -
22B GLN* 2.8 21.7 + - - +
26B SER* 6.0 0.2 - - - -
29B LEU* 3.8 45.3 - - + +
80B LEU* 3.7 11.0 - - + -
81B LEU 2.9 8.7 + - - +
83B SER* 1.3 91.8 + - - +
85B ASN* 1.3 70.5 + - - +
86B VAL* 3.1 12.4 + - + +
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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