Contacts of the helix formed by residues 77 - 99 (chain B) in PDB entry 2P1A
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 THR 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 4.2 11.9 - - - +
41B PHE* 3.9 7.1 - - - -
75B PRO 3.6 0.4 - - - -
76B GLU* 1.3 87.7 - - + +
78B ILE* 1.3 58.6 + - - +
79B ALA* 3.8 8.5 + - - +
80B GLN* 3.0 35.2 + - - +
81B MSE 3.0 32.1 + - - +
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Residues in contact with ILE 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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21B LEU* 3.6 26.0 - - + +
22B ASP* 5.0 1.1 - - - +
24B TYR 3.9 11.7 - - - +
25B THR* 3.7 8.3 - - - -
26B GLU* 3.5 33.8 + - + +
29B LEU* 3.8 20.0 - - + -
41B PHE* 4.4 8.9 - - + -
77B THR* 1.3 69.8 - - - +
79B ALA* 1.3 64.1 + - - +
81B MSE 3.5 12.4 + - - +
82B GLN* 3.1 45.0 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 3.2 8.4 + - - +
78B ILE* 1.3 78.1 - - - +
80B GLN* 1.3 57.9 + - - +
82B GLN* 3.2 9.6 + - - +
83B LYS* 2.9 40.1 + - + +
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN 5.4 2.2 + - - -
74B THR 4.6 2.2 + - - -
75B PRO* 3.6 23.0 - - + +
76B GLU* 3.4 25.3 + - - +
77B THR* 3.0 33.6 + - - +
79B ALA* 1.3 74.7 - - - +
81B MSE 1.3 58.5 + - - +
82B GLN 3.4 0.2 - - - -
83B LYS* 3.9 18.9 - - + +
84B THR* 2.6 39.0 + - - +
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Residues in contact with MSE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.1 21.1 - - + -
29B LEU* 5.2 0.4 - - - -
41B PHE* 3.1 59.9 - - + +
44B TYR* 3.9 19.5 - - + +
45B ALA* 3.3 22.2 - - + +
48B SER* 3.3 16.4 - - - +
75B PRO* 3.5 20.2 - - + +
77B THR 3.0 14.6 + - - +
78B ILE* 3.5 20.6 - - - +
80B GLN* 1.3 76.5 - - - +
82B GLN* 1.3 58.4 + - - +
85B MSE 3.0 28.6 + - + +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.1 39.5 - - + +
21B LEU* 3.7 18.1 - - + +
22B ASP* 3.0 27.5 + - - +
78B ILE* 3.1 32.1 + - - +
79B ALA* 3.6 9.5 - - - +
81B MSE 1.3 78.4 - - - +
83B LYS* 1.3 64.0 - - + +
85B MSE 4.0 4.6 - - - +
86B ILE* 3.2 30.9 + - + +
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Residues in contact with LYS 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 ALA* 2.9 23.5 + - + +
80B GLN* 4.1 21.3 - - - +
82B GLN* 1.3 77.1 - - + +
84B THR* 1.3 57.7 + - - +
86B ILE* 3.5 4.1 + - - +
87B GLN* 3.1 49.7 + - - +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.5 18.8 - - - +
49B LEU* 3.7 24.5 - - + -
52B HIS* 3.3 19.7 + - + +
73B GLN 5.2 2.0 + - - +
75B PRO* 4.0 10.3 - - + +
80B GLN* 2.6 25.1 + - - +
81B MSE 3.8 3.1 - - - -
83B LYS* 1.3 74.7 - - - +
85B MSE 1.3 58.3 + - - +
87B GLN* 3.3 9.2 + - - -
88B GLY* 2.9 26.2 + - - -
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Residues in contact with MSE 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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14B VAL* 4.2 22.9 - - + +
17B SER* 4.0 14.4 - - - -
18B ILE* 4.2 9.4 - - + -
21B LEU* 4.9 5.6 - - + -
44B TYR* 4.4 18.4 - - + +
47B LEU* 4.3 11.0 - - + -
48B SER* 3.4 46.8 + - - +
51B CYS* 4.8 4.5 - - - +
81B MSE 3.0 18.2 + - + +
82B GLN* 4.0 4.5 - - - +
84B THR* 1.3 75.6 - - - +
86B ILE* 1.3 57.5 + - - +
88B GLY* 4.0 1.1 - - - -
89B TYR* 3.1 27.5 + - - +
129B PHE* 3.9 29.8 - - + -
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Residues in contact with ILE 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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11B LYS* 3.5 27.6 - - - +
14B VAL* 3.9 6.5 - - + -
15B ASP* 4.5 1.8 - - - +
18B ILE* 3.4 27.1 - - + -
82B GLN* 3.2 19.9 + - + +
83B LYS* 3.9 5.2 - - - +
85B MSE 1.3 73.1 - - - +
87B GLN* 1.3 61.9 + - + +
89B TYR* 3.3 4.1 + - - +
90B ASP* 2.9 43.5 + - - +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 3.9 13.8 + - + +
83B LYS* 3.1 39.0 + - - +
84B THR* 3.7 10.7 + - - +
86B ILE* 1.3 79.0 - - + +
88B GLY* 1.3 57.5 + - - +
90B ASP* 3.5 8.0 + - - +
91B LEU* 3.0 27.9 + - - +
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Residues in contact with GLY 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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51B CYS* 3.4 19.4 - - - +
52B HIS* 3.3 28.4 - - - -
55B LEU* 5.4 0.3 - - - +
84B THR 2.9 13.1 + - - -
85B MSE 4.0 0.4 - - - -
86B ILE 3.3 0.2 - - - -
87B GLN* 1.3 73.8 - - - +
89B TYR* 1.3 60.7 + - - +
91B LEU* 3.4 3.1 + - - +
92B LEU* 2.9 30.8 + - - +
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.3 41.5 + - + +
8B HIS* 4.5 0.7 + - - -
10B LEU* 3.9 25.4 - - + -
11B LYS* 3.7 45.1 - - + +
14B VAL* 4.3 13.7 - - + -
51B CYS* 3.7 7.9 - - - +
85B MSE 3.1 17.2 + - - +
86B ILE* 3.3 6.3 + - - +
88B GLY* 1.3 76.8 - - - +
90B ASP* 1.3 65.5 + - - +
92B LEU* 3.3 1.6 + - - +
93B SER* 2.8 59.2 + - - -
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Residues in contact with ASP 90 (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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11B LYS* 5.2 1.6 + - - -
86B ILE* 2.9 35.6 + - - +
87B GLN* 3.7 7.8 - - - +
88B GLY 3.3 0.2 - - - -
89B TYR* 1.3 86.3 - - - +
91B LEU* 1.3 58.0 + - - +
93B SER* 3.6 5.8 - - - -
94B LYS* 3.0 47.1 + - + +
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Residues in contact with LEU 91 (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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52B HIS* 4.3 21.8 - - + +
55B LEU* 3.5 21.1 - - + -
87B GLN 3.0 17.8 + - - +
88B GLY* 3.9 4.7 - - - +
90B ASP* 1.3 75.2 - - - +
92B LEU* 1.3 59.4 + - - +
94B LYS* 4.1 5.2 - - + +
95B THR* 2.7 39.2 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.5 1.6 - - + -
10B LEU* 3.3 32.8 - - + -
51B CYS* 4.0 16.6 - - + +
55B LEU* 4.0 29.8 - - + +
58B LEU* 5.3 0.9 - - + -
88B GLY 2.9 17.3 + - - +
89B TYR* 3.7 3.8 - - - +
91B LEU* 1.3 76.8 - - - +
93B SER* 1.3 57.1 + - - +
95B THR* 3.5 3.1 + - - -
96B PHE* 2.9 57.5 + - + +
122B LEU* 4.5 6.5 - - + -
125B ILE* 3.9 26.9 - - + -
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Residues in contact with SER 93 (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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7B LEU* 3.7 25.5 - - - +
89B TYR* 2.8 47.5 + - - -
90B ASP* 3.2 10.2 + - - -
92B LEU* 1.3 71.7 - - - +
94B LYS* 1.3 63.9 + - - +
96B PHE* 3.1 1.7 + - - -
97B LEU* 2.8 42.9 + - - +
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Residues in contact with LYS 94 (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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90B ASP* 3.0 34.4 + - + +
91B LEU* 4.1 5.8 - - + +
93B SER* 1.3 80.4 + - - +
95B THR* 1.3 62.1 + - - +
97B LEU* 3.7 13.8 + - + +
98B SER* 3.2 22.7 + - - -
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Residues in contact with THR 95 (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 LEU* 3.9 26.8 - - + +
59B ASN* 5.2 3.4 + - - +
91B LEU* 2.7 28.9 + - - +
92B LEU 3.5 4.7 - - - +
93B SER 3.1 0.2 - - - -
94B LYS* 1.3 77.3 - - - +
96B PHE* 1.3 59.4 + - + +
98B SER* 2.5 32.0 + - - +
99B TYR* 3.2 39.3 + - + +
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Residues in contact with PHE 96 (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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3B VAL* 3.8 22.3 - - + +
7B LEU* 4.2 8.3 - - + -
55B LEU* 5.0 0.2 - - + -
58B LEU* 3.5 32.8 - - + -
92B LEU* 2.9 44.7 + - + +
93B SER 4.0 2.0 - - - +
95B THR* 1.3 77.2 - - + +
97B LEU* 1.3 60.6 + - - +
99B TYR* 3.4 42.6 + + - +
104B LEU* 3.8 16.4 - - + +
118B ARG* 3.2 36.3 - - + -
119B PHE* 4.5 0.2 - - - -
121B TRP* 5.1 1.3 - + - -
122B LEU* 3.8 36.8 - - + -
125B ILE* 5.7 0.2 - - + -
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Residues in contact with LEU 97 (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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0B GLY* 5.3 2.2 - - - +
3B VAL* 4.2 7.2 - - + -
4B GLN* 4.0 27.4 - - + -
7B LEU* 4.0 17.9 - - + -
93B SER* 2.8 32.0 + - - +
94B LYS* 4.0 15.5 - - + +
96B PHE* 1.3 71.6 - - - +
98B SER* 1.3 60.0 + - - +
99B TYR 3.3 4.1 + - - +
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Residues in contact with SER 98 (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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94B LYS 3.2 12.8 + - - -
95B THR* 2.5 24.2 + - - +
97B LEU* 1.3 75.8 - - - +
99B TYR* 1.3 71.0 + - - +
100B SER 3.7 0.2 + - - -
103B GLN* 3.7 7.3 - - - +
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Residues in contact with TYR 99 (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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3B VAL* 6.0 0.2 - - - +
58B LEU* 4.2 4.7 - - - +
59B ASN* 4.0 13.7 + - - -
95B THR* 3.2 35.8 - - + +
96B PHE* 3.4 50.4 + + - +
97B LEU 3.3 5.2 - - - +
98B SER* 1.3 84.0 - - - +
100B SER* 1.3 65.0 + - - +
101B ASN* 5.6 0.2 + - - -
103B GLN* 3.3 23.6 - - + -
104B LEU* 4.0 16.6 - - + +
118B ARG* 3.4 51.6 + - + -
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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
------------------------------------------------------------
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