Contacts of the strand formed by residues 29 - 38 (chain A) in PDB entry 3ZVU
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 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 17.0 - - - +
26A ASP* 3.0 34.6 + - - +
27A PRO 3.4 2.4 + - - +
28A GLY* 1.3 80.4 - - - +
30A CYS* 1.3 63.4 + - - +
144A VAL* 4.1 10.0 - - - +
145A VAL 3.2 15.7 - - - -
146A ASP* 3.6 14.1 - - - -
147A MET* 3.7 9.0 - - - +
153A GLU* 5.0 3.3 - - - +
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Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 11.2 - - - -
29A SER* 1.3 75.3 - - - +
31A SER* 1.3 61.0 + - - +
143A TYR* 5.1 0.7 - - - -
144A VAL* 3.2 4.3 - - - +
145A VAL* 2.8 42.1 + - - +
147A MET* 3.9 9.0 - - - -
153A GLU* 3.7 27.4 - - + -
156A THR* 3.7 33.9 - - - -
157A ARG* 3.8 20.0 - - - -
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Residues in contact with SER 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.8 24.4 - - - +
25A LEU* 3.8 17.4 - - - +
30A CYS* 1.3 76.8 - - - +
32A SER* 1.3 60.5 + - - +
143A TYR* 2.5 32.8 - - - -
144A VAL* 3.9 4.7 - - - -
157A ARG* 3.1 23.0 + - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 5.9 0.4 - - - -
31A SER* 1.3 76.8 + - - +
33A LEU* 1.3 62.0 + - - +
34A HIS* 3.7 12.8 - - - -
141A GLU 4.1 0.2 - - - +
142A SER* 3.2 5.9 - - - -
143A TYR* 3.1 40.4 + - - +
157A ARG* 3.6 19.3 + - - +
161A ASP* 3.0 34.5 + - - -
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Residues in contact with LEU 33 (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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1A MET* 4.3 30.9 - - + +
2A ALA* 5.0 14.5 - - + +
17A ILE* 4.0 35.7 - - + -
21A HIS* 3.8 37.2 - - + +
32A SER* 1.3 74.8 - - - +
34A HIS* 1.3 87.0 + - - +
140A LEU* 4.4 9.2 - - + -
141A GLU 3.5 13.2 - - - +
142A SER* 3.9 5.2 - - - -
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Residues in contact with HIS 34 (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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2A ALA* 5.2 1.8 - - - -
32A SER* 3.7 10.7 - - - -
33A LEU* 1.3 86.5 + - - +
35A ALA* 1.3 60.7 + - - +
139A VAL 3.9 0.3 - - - +
140A LEU* 3.3 5.0 - - - +
141A GLU 2.7 39.0 + - - +
143A TYR* 4.2 5.4 - + - -
161A ASP* 2.9 48.1 + - + +
164A VAL* 3.6 24.2 - - + -
165A LYS* 3.7 24.8 - - + +
168A LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 35 (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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2A ALA* 4.0 16.7 - - + +
4A GLU* 5.8 6.9 - - + +
5A LEU* 3.5 32.5 - - + +
34A HIS* 1.3 77.7 - - - +
36A GLN* 1.3 65.9 + - - +
37A ARG 4.2 0.4 - - - +
138A VAL* 4.5 1.3 - - + -
139A VAL 3.3 5.8 - - - +
140A LEU* 3.7 13.5 - - + -
168A LEU* 4.6 3.2 - - - +
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Residues in contact with GLN 36 (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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35A ALA* 1.3 76.8 - - - +
37A ARG* 1.3 84.9 + - - +
38A ILE* 3.8 14.8 + - + +
138A VAL* 3.5 4.2 - - - +
139A VAL* 2.8 42.3 + - + +
165A LYS 4.9 0.3 - - - +
168A LEU* 3.5 44.2 - - + +
169A GLN* 3.9 23.4 + - - +
172A ALA* 4.0 10.6 - - + +
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Residues in contact with ARG 37 (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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4A GLU* 3.0 45.3 + - + +
5A LEU* 4.0 4.5 - - + +
6A THR* 3.6 11.2 - - - +
9A GLU* 2.8 42.5 + - - -
35A ALA* 4.2 1.0 - - - +
36A GLN* 1.3 93.7 + - - +
38A ILE* 1.3 63.4 + - - +
39A HIS* 4.1 32.2 + - + +
136A TRP* 4.3 19.1 - - + +
137A THR 3.9 3.1 - - - +
138A VAL* 4.5 8.9 - - + +
172A ALA* 4.3 2.8 - - - +
176A GLU* 4.4 2.4 - - - +
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Residues in contact with ILE 38 (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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36A GLN* 3.8 14.4 - - + +
37A ARG* 1.3 82.8 - - - +
39A HIS* 1.3 63.0 + - - +
40A ALA 3.0 11.7 + - - +
45A VAL* 3.8 27.8 - - + -
136A TRP* 3.9 2.9 - - - +
137A THR 3.0 32.1 + - - +
139A VAL* 3.8 9.9 - - + -
171A LEU* 3.7 31.4 - - + +
172A ALA* 3.7 34.8 - - + +
175A ALA* 3.9 13.9 - - + -
176A GLU* 3.6 9.2 - - + -
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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