Contacts of the strand formed by residues 29 - 38 (chain F) in PDB entry 4ZHF
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 GLY 29 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.9 10.8 - - - -
21D ASN* 3.7 17.9 - - - +
28F GLN* 1.3 77.4 - - - +
30F LYS* 1.3 62.5 + - - -
31F TRP* 3.8 5.5 + - - -
54F THR 3.8 0.9 - - - +
55F ILE* 3.4 7.8 - - - -
56F TYR* 2.8 35.6 + - - -
140F ARG* 3.5 3.6 - - - -
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.2 21.3 + - + +
29F GLY* 1.3 71.9 - - - -
31F TRP* 1.3 64.4 - - - +
32F TYR* 3.8 21.5 + - + +
53F ALA* 4.1 16.4 - - + -
54F THR 3.8 2.9 - - - -
55F ILE* 4.1 30.5 - - + +
69F VAL* 6.3 0.9 - - - -
140F ARG* 2.9 31.4 + - - +
175F CYS 5.3 0.2 + - - -
176F ILE 2.8 30.6 + - - +
177F ASP* 3.4 24.2 + - - +
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Residues in contact with TRP 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F PHE* 3.0 47.9 + + - -
29F GLY 4.0 1.6 - - - -
30F LYS* 1.3 74.4 - - - +
32F TYR* 1.3 62.8 + - - +
33F VAL* 4.0 0.3 + - - +
53F ALA* 3.3 3.1 - - - +
54F THR* 2.8 37.5 + - - +
56F TYR* 3.9 27.1 - + - -
113F THR* 3.8 4.9 - - - -
115F TYR 3.5 20.4 - - - -
117F GLN 3.6 14.4 - - - -
118F HIS* 3.6 35.7 - - - -
119F ALA* 3.9 0.9 - - + -
138F TYR* 3.4 39.3 - + + -
139F GLY 3.6 17.7 - - - -
140F ARG* 3.4 33.5 - - + +
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Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS* 3.8 20.4 + - + +
31F TRP* 1.3 74.2 - - - +
33F VAL* 1.3 61.9 + - - +
34F VAL* 3.1 5.0 + - + -
51F MET* 4.0 12.3 - - - -
52F TYR 3.9 2.7 - - - -
53F ALA* 4.1 8.1 - - + -
138F TYR* 3.3 5.0 - - - -
139F GLY 2.7 35.9 + - - +
140F ARG 3.4 26.0 - - - -
141F THR* 3.5 24.2 - - - +
142F LYS* 3.9 19.6 - - + -
176F ILE* 3.5 42.8 + - + -
177F ASP* 2.6 27.1 + - - -
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F TRP 5.0 0.4 - - - +
32F TYR* 1.3 70.5 - - - +
34F VAL* 1.3 58.9 + - - +
35F GLY 3.6 21.1 - - - +
36F LEU* 3.9 18.4 - - + -
51F MET* 3.6 17.6 - - - +
52F TYR* 3.0 58.6 + - + +
54F THR* 4.3 4.0 - - - +
136F THR* 3.9 9.4 - - + -
137F LEU 3.8 2.7 - - - -
138F TYR* 3.9 23.6 - - + -
169F PRO* 3.6 14.3 - - + +
203F SO4 4.1 2.9 - - - +
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F TYR 3.8 9.6 - - - +
33F VAL* 1.3 75.0 - - - +
35F GLY* 1.3 57.0 + - - +
51F MET* 4.1 9.9 - - + -
137F LEU* 2.8 17.0 + - + +
139F GLY* 3.9 8.3 - - - +
141F THR 3.8 17.7 - - - +
142F LYS* 3.7 23.6 - - - +
143F GLU* 4.5 1.1 - - - +
144F LEU* 4.1 33.7 - - + +
149F LYS* 4.5 12.6 - - + +
168F PHE* 3.3 16.5 - - + +
169F PRO* 3.4 12.9 - - - +
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Residues in contact with GLY 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 3.6 9.7 - - - +
34F VAL* 1.3 79.9 - - - +
36F LEU* 1.3 61.4 + - - -
136F THR* 3.6 3.5 - - - -
137F LEU* 2.8 40.4 + - - +
152F PHE* 3.7 11.4 - - - -
167F VAL 3.5 8.1 - - - -
168F PHE* 4.0 5.4 - - - -
169F PRO* 4.1 0.9 - - - -
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 3.9 15.0 - - + -
35F GLY* 1.3 71.0 - - - -
37F ALA* 1.3 64.2 + - - +
41F ILE* 3.9 27.9 - - + +
49F GLN* 3.9 25.4 - - - +
52F TYR* 4.1 21.1 - - + +
134F LYS* 4.0 20.2 - - + +
135F ILE 3.6 2.7 - - - +
136F THR* 3.9 21.5 - - - +
152F PHE* 3.7 3.0 - - - -
166F ILE* 3.5 0.9 - - - +
167F VAL* 2.8 48.0 + - + +
169F PRO* 4.8 3.6 - - + -
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Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 1.3 76.7 - - - +
38F GLY* 1.3 58.2 + - - +
41F ILE* 3.9 4.9 - - - -
134F LYS* 3.0 5.5 - - - +
135F ILE* 2.7 40.0 + - + +
152F PHE* 3.8 9.0 - - + -
156F SER* 3.3 27.1 - - - +
161F LEU* 3.9 8.5 - - + -
165F HIS 3.2 12.6 - - - +
166F ILE* 3.8 11.9 - - + -
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Residues in contact with GLY 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ALA* 1.3 76.4 - - - +
39F ASN* 1.3 58.1 + - - -
40F ALA 3.2 5.6 - - - -
41F ILE* 3.1 19.4 + - - +
133F PHE 3.2 13.7 - - - -
134F LYS* 3.9 1.8 - - - -
161F LEU* 3.5 17.5 - - - +
165F HIS* 3.1 28.4 + - - +
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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