Contacts of the strand formed by residues 108 - 117 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TRP* 3.6 7.3 - - - -
25B SER* 3.3 22.2 - - - +
27B SER* 4.2 10.1 - - - +
66B PHE* 4.0 28.0 - - + -
101B LEU* 3.7 3.3 - - - -
102B THR* 2.9 51.2 + - + +
106B HIS* 3.5 22.4 + - + +
107B ARG* 1.3 79.7 - - - +
109B VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 109 (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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12B ILE* 3.8 24.5 - - + -
17B ALA* 3.8 2.0 - - + -
20B LEU* 4.5 11.7 - - + -
24B TRP* 4.1 2.6 - - + -
25B SER 2.9 9.4 + - - +
26B HIS* 3.3 37.1 - - + +
27B SER 3.1 22.2 + - - +
99B SER* 4.1 3.1 - - - -
100B HIS 3.3 10.8 - - - +
101B LEU* 4.0 11.0 - - + -
108B VAL* 1.3 73.8 - - - +
110B ALA* 1.3 61.1 + - - +
111B HIS* 3.5 24.0 + - + +
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Residues in contact with ALA 110 (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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27B SER* 3.5 16.8 - - - +
29B HIS* 5.5 0.7 - - - +
99B SER* 3.3 2.7 - - - -
100B HIS* 2.7 43.8 + - + +
102B THR* 4.2 8.7 - - + -
108B VAL 4.0 0.6 - - - -
109B VAL* 1.3 70.5 - - - +
111B HIS* 1.3 63.1 + - - +
112B LEU 3.9 0.3 + - - -
168B THR* 3.6 32.5 - - + -
172B GLN* 3.6 12.2 + - - +
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Residues in contact with HIS 111 (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 ARG* 5.4 2.0 - - + +
17B ALA* 3.6 16.6 - - + -
18B MET* 3.8 9.2 - - + -
26B HIS* 3.0 26.2 + - + -
27B SER 2.7 24.8 + - - +
28B CYS* 3.4 12.4 - - - -
29B HIS* 3.0 26.3 + - - +
74B LEU* 3.6 31.8 - - + +
96B TYR* 4.4 4.1 - - + -
98B SER 3.5 4.3 - - - +
99B SER* 2.7 26.4 + - - +
109B VAL* 3.5 26.5 - - + +
110B ALA* 1.3 73.3 - - - +
112B LEU* 1.3 59.2 + - - +
113B TYR* 4.2 10.4 - - + -
172B GLN* 4.1 3.8 + - - -
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Residues in contact with LEU 112 (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 HIS* 3.5 12.8 - - + +
31B MET* 4.4 12.6 - - + +
62B PHE* 4.5 8.3 - - + -
96B TYR* 3.8 1.4 - - - -
97B LEU* 2.8 55.3 + - + +
98B SER* 2.8 30.3 + - - +
100B HIS* 5.5 0.2 - - - +
110B ALA 3.9 0.4 + - - +
111B HIS* 1.3 73.6 - - - +
113B TYR* 1.3 70.5 + - - +
114B ALA* 5.6 0.2 - - + -
172B GLN* 3.7 56.5 - - + +
175B PHE* 4.6 3.4 - - + -
176B ALA* 4.0 7.2 - - + -
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Residues in contact with TYR 113 (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 ARG* 3.2 12.4 + - - -
28B CYS* 4.0 22.0 - - + -
29B HIS 2.7 15.4 + - - +
30B ALA* 3.2 2.5 - - - -
31B MET* 2.7 31.0 + - - -
74B LEU* 3.3 18.9 - - + +
75B GLU* 2.5 36.8 + - + -
78B LEU* 3.6 23.8 - - + -
91B LEU* 3.9 17.9 - - + -
92B THR 3.7 17.5 - - - -
95B ASP* 3.3 8.5 - - + +
96B TYR* 3.6 27.1 - + + -
111B HIS* 4.2 13.5 - - + -
112B LEU* 1.3 83.9 - - - +
114B ALA* 1.3 56.9 + - - +
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Residues in contact with ALA 114 (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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31B MET* 3.3 16.4 - - + +
33B TYR* 4.4 2.7 - - + -
91B LEU* 5.3 1.3 - - - -
95B ASP* 2.8 30.9 + - - +
97B LEU* 3.9 25.1 - - + +
112B LEU* 5.6 0.2 - - + -
113B TYR* 1.3 76.0 - - - +
115B ARG* 1.3 60.7 + - - +
176B ALA* 5.8 0.2 - - + -
180B LEU* 4.1 23.1 - - + -
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Residues in contact with ARG 115 (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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31B MET 3.2 5.9 + - - -
32B LEU* 3.7 13.9 - - + +
33B TYR* 3.4 23.2 + - - -
89B LEU* 4.4 12.7 - - + +
90B ARG 3.3 23.0 + - - -
91B LEU* 3.6 23.6 - - + +
92B THR* 4.4 6.9 + - - +
95B ASP* 2.8 39.4 + - - +
114B ALA* 1.3 77.6 - - - +
116B GLN* 1.3 70.0 + - - +
117B LEU* 3.6 25.8 + - + +
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Residues in contact with GLN 116 (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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33B TYR* 3.4 42.8 + - + +
34B ALA* 4.9 0.9 - - - -
35B ALA* 4.5 22.0 - - - +
48B PHE* 5.2 4.2 - - - -
115B ARG* 1.3 84.1 - - - +
117B LEU* 1.3 71.5 + - - +
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Residues in contact with LEU 117 (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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32B LEU* 4.3 12.1 - - + -
33B TYR 2.8 9.6 + - - +
34B ALA* 3.1 20.7 - - - +
35B ALA 4.2 2.1 + - - -
89B LEU* 4.5 15.0 - - + -
115B ARG* 3.7 36.3 - - + +
116B GLN* 1.3 84.9 + - - +
118B THR* 1.3 70.5 + - - +
121B GLN* 3.6 22.7 - - + +
122B LEU* 3.7 28.5 - - + +
125B VAL* 4.1 23.1 - - + -
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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