Contacts of the strand formed by residues 108 - 117 (chain A) in PDB entry 5ZCJ
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 VAL 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TRP* 3.4 11.8 - - - -
25A SER* 3.4 21.3 - - - +
27A SER* 4.5 8.1 - - - +
66A PHE* 3.9 27.1 - - + -
101A LEU* 3.7 0.3 - - - -
102A THR* 3.0 50.9 + - + +
106A HIS* 3.2 22.0 + - + +
107A ARG* 1.3 79.3 - - - +
109A VAL* 1.3 69.7 + - - +
1551C GLU* 4.7 5.2 - - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.9 24.5 - - + -
17A ALA* 4.1 4.0 - - + -
20A LEU* 3.9 18.6 - - + -
24A TRP* 3.9 1.7 - - + -
25A SER 2.9 10.2 + - - +
26A HIS* 3.3 36.3 - - + +
27A SER 3.1 22.9 + - - +
99A SER* 4.2 2.5 - - - -
100A HIS 3.4 9.6 - - - +
101A LEU* 4.1 5.8 - - + -
108A VAL* 1.3 75.3 - - - +
110A ALA* 1.3 63.0 + - - +
111A HIS* 3.6 21.5 + - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.5 16.6 - - - +
29A HIS* 5.6 0.2 - - + -
98A SER 4.0 0.2 - - - +
99A SER* 3.3 1.7 - - - -
100A HIS* 2.7 43.7 + - + +
102A THR* 4.1 9.0 - - + -
108A VAL 4.1 0.4 - - - -
109A VAL* 1.3 72.2 - - - +
111A HIS* 1.3 63.1 + - - +
112A LEU 3.8 0.9 + - - -
168A THR* 3.7 31.0 - - + -
172A GLN* 3.7 12.2 + - - +
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Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 5.8 0.4 - - - -
17A ALA* 3.7 17.0 - - + -
18A MET* 3.8 8.7 - - + -
26A HIS* 3.0 27.9 + - + -
27A SER 2.8 24.6 + - - +
28A CYS* 3.4 14.2 - - - -
29A HIS* 3.0 26.5 + - - +
74A LEU* 3.7 29.5 - - + +
96A TYR* 4.3 4.4 - - + -
98A SER 3.5 4.5 - - - +
99A SER* 2.6 27.8 + - - +
109A VAL* 3.6 25.3 - - + +
110A ALA* 1.3 71.6 - - - +
112A LEU* 1.3 59.2 + - - +
113A TYR* 4.2 11.7 - - + -
172A GLN* 4.4 3.4 + - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS 3.7 10.8 - - - +
31A MET* 4.4 12.3 - - + +
62A PHE* 4.7 5.8 - - + -
96A TYR* 4.1 1.2 - - - -
97A LEU* 2.9 48.3 + - + +
98A SER* 2.8 25.9 + - - +
100A HIS* 5.3 1.1 - - + +
110A ALA 3.8 1.7 + - - +
111A HIS* 1.3 73.4 - - - +
113A TYR* 1.3 79.9 + - - +
172A GLN* 3.8 57.4 - - + +
175A PHE* 4.2 11.4 - - + -
176A ALA* 4.2 6.1 - - + -
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.6 4.5 + - - -
28A CYS* 4.2 19.5 - - + -
29A HIS 2.8 16.1 + - - +
30A ALA* 3.3 2.1 - - - -
31A MET 2.7 30.6 + - - -
74A LEU* 3.4 18.0 - - - +
75A GLU* 2.4 39.2 + - + -
78A LEU* 3.6 31.6 - - + -
91A LEU* 4.1 12.3 - - + -
92A THR 3.7 13.7 - - - -
95A ASP* 3.3 10.1 - - + +
96A TYR* 3.4 40.3 - + - -
97A LEU* 4.7 0.4 - - - -
111A HIS* 4.2 9.6 - - + -
112A LEU* 1.3 83.9 - - - +
114A ALA* 1.3 57.4 + - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 5.7 0.2 - - - -
31A MET* 3.3 16.2 - - + +
33A TYR* 4.4 2.9 - - + -
91A LEU* 5.6 0.7 - - - -
95A ASP* 2.9 29.8 + - - +
97A LEU* 4.0 19.2 - - + +
113A TYR* 1.3 76.7 - - - +
115A ARG* 1.3 61.3 + - - +
176A ALA* 5.6 0.2 - - + -
180A LEU* 4.0 29.4 - - + -
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET 3.2 6.5 + - - -
32A LEU* 3.6 20.3 - - + +
33A TYR* 3.3 26.2 + - - +
89A LEU* 4.3 11.9 - - - +
90A ARG 3.6 20.6 + - - -
91A LEU* 4.0 12.4 - - + +
92A THR* 4.5 6.9 + - - +
95A ASP* 2.9 43.0 + - + +
114A ALA* 1.3 74.9 - - - +
116A GLN* 1.3 71.4 + - - +
117A LEU* 3.6 29.2 + - + +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 3.3 45.8 + - + +
34A ALA* 4.5 0.7 - - - -
35A ALA* 4.1 24.4 - - - +
48A PHE* 4.8 5.2 - - - -
115A ARG* 1.3 83.7 - - - +
117A LEU* 1.3 70.3 + - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.4 18.8 - - + -
33A TYR 2.8 11.2 + - - +
34A ALA* 3.1 20.4 - - - +
35A ALA 4.4 1.6 + - - -
89A LEU* 4.3 15.9 - - + -
115A ARG* 3.6 39.0 - - + +
116A GLN* 1.3 83.7 + - - +
118A THR* 1.3 71.7 + - - +
121A GLN* 3.4 21.8 - - + +
122A LEU* 4.1 16.8 - - + +
125A VAL* 4.0 27.1 - - + -
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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