Contacts of the strand formed by residues 31 - 34 (chain A) in PDB entry 3S3J
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 LEU 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.9 36.0 - - + +
14A LEU* 3.6 23.7 - - + +
17A ASN* 3.6 34.1 - - + +
27A CYS* 4.4 2.5 - - - -
29A GLU 4.3 0.2 + - - -
30A LYS* 1.3 72.7 - - - +
32A VAL* 1.3 68.9 + - - +
33A VAL* 3.8 12.3 - - + -
39A PHE* 4.1 27.1 - - + -
40A TRP 5.1 0.7 - - - +
41A LEU* 6.3 0.7 - - + -
134A HIS 4.1 5.4 + - - +
135A PHE* 3.1 25.2 - - + -
136A ILE* 2.8 24.9 + - - +
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Residues in contact with VAL 32 (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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18A GLY* 5.0 0.3 - - - -
23A THR* 2.9 27.5 + - + -
26A LEU* 3.5 40.8 - - + +
27A CYS* 3.7 8.5 - - - -
30A LYS* 3.6 7.9 + - + +
31A LEU* 1.3 81.3 - - - +
33A VAL* 1.3 71.5 + - - +
136A ILE* 3.4 17.9 - - + +
138A LEU* 3.7 31.0 - - + -
190A LEU* 4.1 20.2 - - + -
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Residues in contact with VAL 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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17A ASN* 4.4 2.0 - - + -
21A HIS* 3.8 22.9 - - + +
23A THR* 4.5 1.1 - - - -
31A LEU* 3.8 19.5 - - + -
32A VAL* 1.3 81.3 - - - +
34A ARG* 1.3 64.4 + - - +
39A PHE* 3.9 39.0 - - + -
135A PHE* 3.9 18.8 - - + -
136A ILE 2.8 18.1 + - - +
137A LEU* 3.4 17.3 - - + -
138A LEU* 2.9 27.5 + - - +
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Residues in contact with ARG 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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21A HIS* 2.7 50.1 + - + +
22A HIS 2.8 21.6 + - - -
23A THR* 3.6 14.2 - - + +
26A LEU* 4.8 0.4 - - - +
33A VAL* 1.3 81.7 - - - +
35A ARG* 1.3 65.3 + - - +
37A GLN* 3.8 5.9 - - - +
39A PHE* 5.5 1.0 - - - -
106A THR* 4.4 0.5 + - - -
137A LEU* 3.8 5.3 - - - +
138A LEU* 3.5 17.5 - - + +
139A PHE 3.2 23.5 + - - +
140A ASN* 3.1 30.7 + - + +
142A TRP* 3.6 25.9 - - - -
160A VAL* 4.4 2.8 - - - +
161A LEU* 4.1 12.3 - - - +
185A PHE* 4.3 14.6 - - - -
289A ARG 5.5 0.2 + - - -
290A CYS 5.1 0.4 + - - -
292A GLY* 3.7 21.4 + - - -
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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