Contacts of the helix formed by residues 71 - 87 (chain B) in PDB entry 2ZPB
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 6.0 2.9 - - + -
69B MET 3.8 7.0 - - - +
70B THR* 1.4 85.7 - - + +
72B TYR* 1.3 68.3 + - - +
73B TYR 4.7 2.2 - - - +
74B GLU* 3.1 37.6 + - + +
75B ARG* 3.1 10.4 + - - +
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Residues in contact with TYR 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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112A CSD 4.5 2.9 - - - -
113A SER* 2.6 33.1 + - - -
125A THR* 6.5 0.7 - - + -
128A LYS* 3.5 44.4 - - + +
301A NO 4.4 2.3 + - - -
37B TYR* 2.5 37.3 + + - -
70B THR 3.6 0.8 + - - -
71B PRO* 1.3 72.2 - - - +
73B TYR* 1.3 85.7 + + + +
75B ARG* 3.0 44.5 + - - +
76B TYR* 3.1 50.7 - + - -
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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
----------------------------------------------------------
122A LEU* 3.7 18.5 - - - +
123A PRO* 5.0 0.9 + - - +
128A LYS* 3.6 26.7 + - - -
27B THR 4.6 7.5 + - - -
28B PHE* 3.6 25.2 - + - -
32B TRP* 3.9 22.4 - - + -
33B GLU* 3.7 45.8 - - + +
36B PRO* 3.6 15.6 - - + +
37B TYR* 3.8 30.1 + + - -
71B PRO* 3.4 2.0 - - - +
72B TYR* 1.3 95.1 - + + +
74B GLU* 1.3 61.5 + - - +
76B TYR* 3.2 4.5 + + - -
77B VAL* 3.1 22.9 + - - +
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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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15A GLN* 3.8 12.6 + - - +
18A VAL* 3.6 29.2 - - + +
21A ARG* 2.8 42.4 + - - +
32B TRP* 3.8 10.2 - - + -
70B THR* 3.5 18.1 + - + +
71B PRO* 3.1 30.8 + - + +
73B TYR* 1.3 76.5 - - - +
75B ARG* 1.3 65.2 + - - +
77B VAL* 3.2 6.3 + - + +
78B ILE* 3.0 23.4 + - + +
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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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112A CSD 5.7 1.2 - - - -
128A LYS 4.6 3.6 + - - -
130A PHE* 3.7 24.0 - - - -
133A ARG* 3.5 23.6 - - - +
59B VAL* 3.7 16.9 - - + +
62B MET* 3.7 19.2 - - - +
67B TYR* 3.7 44.0 + - - -
70B THR* 2.8 46.6 + - + -
71B PRO* 3.1 7.6 + - - +
72B TYR* 3.0 46.6 + - - +
74B GLU* 1.3 76.0 - - - +
76B TYR* 1.3 62.8 + - + +
78B ILE* 3.4 3.2 + - - +
79B GLY* 2.8 25.8 + - - -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A CSD 3.6 25.2 + - - +
113A SER* 4.6 0.2 + - - -
301A NO 4.6 2.3 + - - -
36B PRO* 3.6 24.2 - - + -
37B TYR* 4.8 13.2 - + + -
40B MET* 5.4 3.6 - - - -
55B VAL* 3.8 28.0 - - + -
56B ARG* 5.5 5.5 - - + -
59B VAL* 3.9 26.5 - - + +
72B TYR* 3.1 63.5 + + - -
73B TYR* 3.2 3.1 + - + +
74B GLU 3.1 1.0 - - - -
75B ARG* 1.3 84.7 + - + +
77B VAL* 1.3 58.4 + - - +
79B GLY* 4.2 0.9 - - - +
80B VAL* 2.9 36.2 + - + +
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Residues in contact with VAL 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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18A VAL* 5.2 4.3 - - + +
21A ARG* 4.3 5.2 - - + +
22A ALA* 3.9 32.5 - - + +
25A LEU* 3.8 13.5 - - + +
32B TRP* 3.7 22.0 - - + -
35B LEU* 5.6 0.4 - - + -
36B PRO* 3.8 19.3 - - + +
73B TYR 3.1 13.8 + - - +
74B GLU* 3.2 10.0 + - + +
76B TYR* 1.3 76.0 - - - +
78B ILE* 1.3 65.6 + - + +
81B ALA* 3.0 23.9 + - - +
103B PHE* 4.0 19.7 - - + -
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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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15A GLN* 4.0 0.9 - - - +
21A ARG* 3.9 25.6 - - - +
62B MET* 3.8 22.2 - - + -
66B HIS* 3.7 28.0 - - + +
70B THR* 4.2 2.0 - - + -
74B GLU* 3.0 25.3 + - + +
75B ARG* 3.6 6.7 - - - +
77B VAL* 1.3 76.1 - - + +
79B GLY* 1.3 55.3 + - - +
81B ALA* 3.5 1.7 + - - +
82B THR* 2.7 36.7 + - - -
103B PHE* 4.4 10.8 - - + -
104B PRO 3.9 20.0 - - - +
105B LEU* 4.1 2.4 - - - +
106B SER* 3.9 24.2 - - - +
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Residues in contact with GLY 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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55B VAL* 5.6 0.4 - - - -
58B VAL* 3.4 36.7 - - - +
59B VAL* 4.3 7.4 - - - -
75B ARG 2.8 21.2 + - - -
76B TYR* 3.8 1.1 - - - -
77B VAL 3.3 0.2 - - - -
78B ILE* 1.3 73.3 - - - +
80B VAL* 1.3 63.3 + - - +
82B THR* 3.2 2.8 + - - -
83B LEU* 3.0 19.6 + - - +
106B SER* 4.6 3.8 + - - -
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Residues in contact with VAL 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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25A LEU* 4.0 19.1 - - + -
36B PRO* 4.0 20.2 - - + +
39B LEU* 4.3 16.6 - - + +
40B MET* 4.1 15.5 - - + -
50B PHE* 4.3 7.6 - - + -
55B VAL* 4.6 13.5 - - + -
76B TYR* 2.9 25.9 + - + +
79B GLY* 1.3 70.8 - - - +
81B ALA* 1.3 65.3 + - - +
83B LEU* 3.2 8.6 + - - +
84B MET* 3.0 43.8 + - + +
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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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25A LEU* 3.9 18.1 - - + +
77B VAL 3.0 19.4 + - - +
78B ILE 3.7 3.8 - - - +
80B VAL* 1.3 77.4 - - - +
82B THR* 1.3 61.9 + - - +
84B MET* 3.3 3.5 + - - +
85B VAL* 3.1 26.7 + - - +
95B LEU* 4.0 14.3 - - + +
103B PHE* 3.7 28.5 - - + -
105B LEU* 4.0 4.3 - - + -
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Residues in contact with THR 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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58B VAL* 3.6 18.2 - - + -
78B ILE 2.7 23.0 + - - -
79B GLY 3.2 5.1 + - - -
81B ALA* 1.3 75.0 - - - +
83B LEU* 1.3 58.8 + - - +
85B VAL* 3.2 3.6 + - - +
86B GLU* 2.8 50.6 + - + +
105B LEU* 3.2 20.1 - - + +
106B SER* 2.9 38.1 + - - +
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Residues in contact with LEU 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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50B PHE* 3.8 28.3 - - + -
54B GLU* 3.8 36.1 - - + +
55B VAL* 3.8 23.6 - - + +
58B VAL* 3.8 17.7 - - + -
61B ARG* 4.2 4.0 - - - +
79B GLY 3.0 14.9 + - - +
80B VAL* 3.2 6.9 + - - +
82B THR* 1.3 77.2 - - - +
84B MET* 1.3 58.8 + - - +
86B GLU* 3.7 18.7 - - - +
87B LYS* 2.8 50.3 + - - +
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Residues in contact with MET 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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25A LEU* 4.4 3.4 - - + -
29A LEU* 3.9 31.6 - - + -
39B LEU 4.3 4.3 - - - +
42B ALA* 5.8 0.7 - - + -
43B GLY* 4.1 14.8 - - - +
47B LEU* 4.3 8.5 - - + -
49B ALA* 5.1 1.3 - - - -
50B PHE* 3.6 31.2 - - + -
80B VAL* 3.0 28.3 + - + +
81B ALA 3.6 7.2 - - - +
83B LEU* 1.3 75.3 - - - +
85B VAL* 1.3 59.5 + - - +
87B LYS* 4.8 0.2 - - - -
88B GLY 3.4 2.1 + - - -
89B ILE* 2.9 47.9 + - - +
90B LEU* 3.0 34.0 + - + -
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Residues in contact with VAL 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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81B ALA 3.1 14.7 + - - +
82B THR* 3.6 6.1 - - + +
84B MET* 1.3 75.4 - - - +
86B GLU* 1.3 66.9 + - + +
88B GLY* 3.0 14.6 + - - -
90B LEU* 3.3 17.3 - - + +
91B THR* 3.9 1.3 - - - -
92B GLN* 3.8 30.1 - - + +
95B LEU* 3.8 18.2 - - + -
105B LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 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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61B ARG* 2.8 45.7 + - - -
82B THR* 2.8 36.2 + - + +
83B LEU* 3.8 16.5 - - + +
85B VAL* 1.3 75.6 - - + +
87B LYS* 1.3 65.4 + - + +
88B GLY 3.2 0.9 + - - -
106B SER 5.0 0.3 - - - +
107B ARG 4.9 0.2 - - - -
108B PRO* 4.4 9.2 - - - +
109B SER 4.9 0.2 + - - -
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Residues in contact with LYS 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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49B ALA* 3.3 30.2 + - + +
50B PHE* 4.3 9.6 - - + -
54B GLU* 2.8 32.5 + - - -
83B LEU* 2.8 29.2 + - - +
84B MET* 4.8 0.2 - - - -
86B GLU* 1.3 79.8 - - + +
88B GLY* 1.3 60.8 + - - +
89B ILE* 3.3 24.3 + - + +
169B HIS 5.2 1.6 + - - -
170B GLY* 4.8 6.3 - - - -
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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