Contacts of the helix formed by residues 51 - 61 (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 SER 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.9 8.7 - - - -
50B PHE* 1.3 74.8 - - - +
52B VAL* 1.3 65.0 + - - +
53B ASP* 3.5 5.9 + - - +
54B GLU* 3.0 36.5 + - - +
55B VAL* 3.3 14.0 + - - +
167B ILE* 3.4 43.7 + - - +
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Residues in contact with VAL 52 (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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90A GLN* 4.6 14.8 - - - +
40B MET* 4.6 20.4 - - + -
41B PHE* 4.9 13.0 - - + -
44B VAL* 3.9 22.9 - - + +
51B SER* 1.3 73.2 - - - +
53B ASP* 1.3 66.0 + - - +
55B VAL* 3.0 19.6 + - + +
56B ARG* 3.0 42.3 + - + +
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Residues in contact with ASP 53 (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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165A GLU* 5.0 8.1 - - - +
51B SER* 3.2 11.9 + - - +
52B VAL* 1.3 80.4 + - - +
54B GLU* 1.3 56.2 + - - +
56B ARG* 3.2 22.1 + - - +
57B TYR* 3.0 28.6 + - - +
139B HIS* 3.9 10.7 + - + -
141B ARG* 5.6 1.0 - - - +
162B PRO* 4.8 3.6 - - - +
164B PRO* 3.7 19.8 - - - +
167B ILE* 3.4 27.1 - - - +
168B GLY* 3.6 22.4 - - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.2 18.5 - - + -
51B SER* 3.0 39.3 + - - +
53B ASP* 1.3 75.7 - - - +
55B VAL* 1.3 57.5 + - - +
57B TYR* 3.5 1.4 + - - +
58B VAL* 2.9 30.7 + - - +
61B ARG* 5.1 0.7 + - - -
83B LEU* 3.8 12.6 - - + +
87B LYS* 2.8 31.0 + - - -
167B ILE 3.4 9.6 - - - +
168B GLY 3.3 22.7 - - - +
169B HIS 3.9 2.3 - - - -
170B GLY* 3.6 22.4 + - - -
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Residues in contact with VAL 55 (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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40B MET* 3.8 29.8 - - + -
50B PHE* 3.6 27.8 - - + -
51B SER 3.6 13.0 - - - +
52B VAL* 3.0 9.5 + - + +
54B GLU* 1.3 73.5 - - - +
56B ARG* 1.3 66.6 + - + +
58B VAL* 3.3 12.1 - - + +
59B VAL* 3.2 24.6 + - + +
76B TYR* 3.8 28.3 - - + -
80B VAL* 4.6 13.5 - - + +
83B LEU* 3.8 4.5 - - + -
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 4.1 6.1 + - - +
112A CSD 3.0 30.3 + - - +
114A CSO 2.9 23.2 + - - -
164A ALA 5.0 2.8 + - - -
165A GLU* 4.6 12.5 + - - -
167A ARG* 3.5 17.2 - - - +
301A NO 4.6 1.6 + - - -
52B VAL* 3.0 39.8 + - + +
53B ASP* 3.5 26.7 + - - +
55B VAL* 1.3 77.4 - - + +
57B TYR* 1.3 64.2 + - - +
59B VAL* 3.3 5.9 + - - +
60B GLU* 3.0 28.6 + - - +
76B TYR* 5.5 6.3 - - + -
139B HIS* 3.8 12.1 + - + -
141B ARG* 3.5 29.4 - - - +
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Residues in contact with TYR 57 (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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1B MET* 3.9 13.9 - - - -
53B ASP 3.0 16.1 + - - +
54B GLU 3.9 1.8 - - - +
55B VAL 3.2 0.2 - - - -
56B ARG* 1.3 76.7 - - - +
58B VAL* 1.3 62.6 + - - +
60B GLU* 3.1 22.0 + - + +
61B ARG* 2.9 59.8 + - + +
109B SER* 2.7 27.6 + - - -
110B GLU 4.1 3.6 + - - -
111B SER 4.3 1.6 + - - -
137B PRO 4.3 2.6 + - - -
138B GLY* 3.7 11.2 - - - -
139B HIS* 3.6 27.8 + - + -
168B GLY 3.5 21.5 - - - +
169B HIS* 3.2 28.5 - + - -
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Residues in contact with VAL 58 (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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54B GLU 2.9 17.5 + - - +
55B VAL* 3.3 13.5 - - + +
57B TYR* 1.3 76.0 - - - +
59B VAL* 1.3 63.3 + - - +
61B ARG* 3.2 38.7 + - - +
79B GLY* 3.4 28.3 - - - +
82B THR* 3.6 34.5 - - + -
83B LEU* 3.8 15.0 - - + -
106B SER* 2.8 28.0 + - - +
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Residues in contact with VAL 59 (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 6.4 0.2 - - + -
55B VAL* 3.2 14.4 + - + +
56B ARG* 3.7 7.4 - - - +
58B VAL* 1.3 72.5 - - + +
60B GLU* 1.3 65.3 + - + +
61B ARG 3.0 1.3 - - - -
62B MET* 3.1 25.7 + - - +
67B TYR* 3.7 25.8 - - + +
75B ARG* 3.7 40.8 - - + +
76B TYR* 3.9 34.1 - - + +
79B GLY* 4.3 8.7 - - - -
106B SER* 4.7 0.7 - - - -
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Residues in contact with GLU 60 (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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111A LEU* 5.2 2.1 - - - +
1B MET* 3.8 26.0 + - - +
3B GLY* 5.5 2.1 - - - -
5B HIS* 3.5 55.9 + - + +
56B ARG* 3.0 19.8 + - - +
57B TYR* 3.3 16.4 - - + +
59B VAL* 1.3 75.8 - - + +
61B ARG* 1.3 59.9 + - - +
62B MET 3.3 6.8 + - - +
67B TYR* 5.0 2.5 - - - -
139B HIS* 3.0 42.2 + - - -
140B ILE 4.7 3.8 + - - +
141B ARG* 4.2 9.7 + - - -
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Residues in contact with ARG 61 (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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1B MET* 4.5 12.1 - - + -
54B GLU 5.1 0.2 + - - -
57B TYR* 2.9 55.1 + - + +
58B VAL* 3.4 40.7 - - - +
59B VAL 3.0 0.8 - - - -
60B GLU* 1.3 75.8 - - - +
62B MET* 1.3 66.5 + - - +
63B GLU 3.4 0.5 + - - -
82B THR* 4.6 0.8 - - - +
83B LEU* 4.2 5.7 - - - +
86B GLU* 2.8 42.0 + - - -
106B SER* 3.8 3.1 - - - -
107B ARG* 2.8 60.1 + - + +
108B PRO 4.2 1.1 - - - +
109B SER* 3.5 30.3 - - - +
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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