Contacts of the strand formed by residues 34 - 37 (chain N) in PDB entry 1G3I
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 34 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N ILE* 4.6 2.0 - - + -
14N VAL* 3.3 46.7 - - + +
15N GLY 3.8 3.4 - - - +
16N GLY* 3.7 17.7 - - - +
32N ARG* 4.6 5.9 - - - +
33N LYS* 1.3 83.0 - - - +
35N ARG* 1.3 70.1 + - - +
43N LEU* 5.1 0.7 - - + -
44N ALA 3.1 16.8 - - - +
45N GLY* 4.3 3.1 - - - -
168N THR* 3.7 25.9 + - - +
170N GLU* 4.2 24.5 - - + +
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Residues in contact with ARG 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ARG* 3.3 59.0 + - - +
34N VAL* 1.3 81.2 - - - +
36N ARG* 1.3 66.7 + - - +
43N LEU* 4.0 3.1 - - - +
44N ALA* 2.8 33.0 + - - +
46N PHE* 4.1 10.3 - - + -
54N PHE* 4.1 23.5 - - - -
57N PHE* 3.5 34.4 - - + -
170N GLU* 5.2 0.4 - - - -
440U SER 3.8 12.5 + - - -
441U ARG* 3.0 30.4 + - - +
443U ILE 3.5 21.0 + - - -
444U LEU* 4.3 5.7 - - - +
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Residues in contact with ARG 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ARG* 1.3 78.7 - - - +
37N LEU* 1.3 63.4 + - - +
40N GLY* 4.2 25.9 + - - +
42N VAL 3.8 4.9 + - - +
43N LEU* 3.6 14.7 - - + +
170N GLU* 3.5 35.3 + - + +
171N GLU 3.0 25.3 + - - +
172N LEU* 3.5 23.6 - - - +
173N PRO 4.9 4.8 + - - -
441U ARG* 3.5 21.8 + - - -
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Residues in contact with LEU 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ARG 4.2 0.4 + - - -
36N ARG* 1.3 74.4 - - - +
38N TYR* 1.3 73.9 + - - +
39N ASN 3.5 1.8 - - - -
40N GLY 3.4 0.6 + - - -
41N LYS 3.1 3.1 + - - -
42N VAL* 2.9 43.5 + - + +
44N ALA* 4.8 4.5 - - + -
57N PHE* 3.8 32.5 - - + +
60N PHE* 4.3 9.2 - - + -
61N GLU* 3.1 47.8 - - + +
64N LEU* 3.9 13.9 - - + -
441U ARG* 3.0 31.4 - - - +
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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