Contacts of the strand formed by residues 29 - 38 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E GLN* 1.3 79.8 - - - +
30E LYS* 1.3 62.4 + - - -
31E TRP* 3.8 5.7 + - - -
54E THR 3.8 0.7 - - - +
55E ILE* 3.4 8.5 - - - -
56E TYR 2.8 35.5 + - - -
57E GLU* 6.2 0.2 - - - -
140E ARG* 3.5 4.0 - - - -
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLY* 1.3 72.1 - - - -
31E TRP* 1.3 64.6 + - - +
32E TYR* 3.8 21.2 + - + +
53E ALA* 4.1 17.5 - - + -
54E THR 3.8 3.4 - - - -
55E ILE* 4.1 28.9 - - + +
69E VAL* 5.4 1.5 - - - +
140E ARG* 2.9 31.6 + - - +
175E CYS 5.3 0.2 + - - -
176E ILE 2.8 34.2 + - - +
177E ASP* 3.6 18.2 + - - +
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Residues in contact with TRP 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E PHE* 3.0 47.8 + + - -
29E GLY 4.0 2.0 - - - -
30E LYS* 1.3 74.8 - - - +
32E TYR* 1.3 63.6 + - - +
33E VAL* 5.0 0.2 - - - +
53E ALA* 3.3 3.1 - - - +
54E THR* 2.8 37.3 + - - +
56E TYR* 3.9 24.5 - + - -
113E THR* 3.8 4.9 - - - -
115E TYR 3.4 20.0 - - - -
117E GLN 3.6 14.1 - - - -
118E HIS* 3.6 35.7 - - - -
119E ALA* 3.9 0.7 - - + -
138E TYR* 3.3 40.8 - + + -
139E GLY 3.6 17.5 - - - -
140E ARG* 3.4 36.2 - - + +
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Residues in contact with TYR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS* 3.8 19.7 + - + +
31E TRP* 1.3 76.0 - - - +
33E VAL* 1.3 62.3 + - - +
34E VAL* 3.1 4.4 + - + -
51E MET* 4.0 12.8 - - - -
52E TYR 3.8 2.2 - - - -
53E ALA* 4.1 7.9 - - + -
138E TYR* 3.3 5.7 - - - -
139E GLY 2.7 34.6 + - - +
140E ARG 3.4 26.5 - - - -
141E THR* 3.5 24.2 - - - +
142E LYS* 3.9 20.1 - - + -
176E ILE* 3.4 41.6 + - + -
177E ASP* 3.2 24.9 + - - -
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TRP 5.0 0.4 - - - +
32E TYR* 1.3 70.9 - - - +
34E VAL* 1.3 58.4 + - - +
35E GLY 3.6 20.9 - - - +
36E LEU* 3.9 18.6 - - + -
51E MET* 3.6 17.0 - - - +
52E TYR* 3.0 57.8 + - + +
54E THR* 4.3 4.9 - - - +
136E THR* 3.9 9.0 - - + -
137E LEU 3.8 3.1 - - - -
138E TYR* 3.9 23.8 - - + -
169E PRO* 3.6 13.9 - - + +
203E SO4 4.1 2.2 - - - +
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E TYR* 3.8 12.1 - - + +
33E VAL* 1.3 74.8 - - - +
35E GLY* 1.3 58.9 + - - +
51E MET* 4.1 10.5 - - + -
137E LEU* 2.8 17.1 + - + +
139E GLY* 3.9 8.3 - - - +
141E THR 3.8 16.2 - - - +
142E LYS 3.7 26.0 - - - +
143E GLU* 5.2 0.2 - - - -
144E LEU* 4.1 31.9 - - + +
149E LYS* 4.5 13.0 - - + +
168E PHE* 3.3 16.5 - - - +
169E PRO* 3.4 13.6 - - - +
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Residues in contact with GLY 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.6 10.0 - - - +
34E VAL* 1.3 80.9 - - - +
36E LEU* 1.3 61.4 + - - -
136E THR* 3.6 4.2 - - - -
137E LEU* 2.8 39.8 + - - +
152E PHE* 3.8 10.5 - - - -
167E VAL 3.5 8.7 - - - -
168E PHE* 4.0 4.9 - - - -
169E PRO* 4.0 0.9 - - - -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.9 12.1 - - + -
35E GLY* 1.3 74.1 - - - +
37E ALA* 1.3 63.6 + - - +
41E ILE* 3.9 28.8 - - + +
49E GLN* 3.9 25.4 - - - +
52E TYR* 4.1 22.4 - - + +
134E LYS* 4.0 20.4 - - + +
135E ILE 3.6 2.7 - - - +
136E THR* 3.9 21.5 - - - +
152E PHE* 3.7 3.0 - - - -
166E ILE* 3.5 1.2 - - - +
167E VAL* 2.8 47.0 + - + +
169E PRO* 4.8 6.1 - - + -
202E 4OL 6.5 0.2 - - - -
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E LEU* 1.3 76.3 - - - +
38E GLY* 1.3 56.8 + - - +
41E ILE* 3.8 5.8 - - - -
134E LYS* 3.0 5.2 - - - +
135E ILE* 2.7 39.6 + - + +
152E PHE* 3.8 7.9 - - + -
156E SER* 3.3 26.7 - - - +
161E LEU* 3.9 9.2 - - + -
165E HIS 3.3 12.1 - - - +
166E ILE* 3.8 12.6 - - + -
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Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ALA* 1.3 75.8 - - - +
39E ASN* 1.3 58.4 + - - -
40E ALA 3.2 5.8 - - - -
41E ILE* 3.1 18.1 + - - +
133E PHE 3.2 13.7 - - - -
134E LYS* 3.9 1.6 - - - -
161E LEU* 3.5 17.5 - - - +
165E HIS* 3.0 28.8 + - - +
202E 4OL 4.8 0.2 - - - -
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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