Contacts of the strand formed by residues 30 - 34 (chain A) in PDB entry 2XFN
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 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A CYS* 4.7 0.2 - - - -
7A VAL* 3.3 13.7 - - + +
9A VAL* 5.2 2.0 - - + -
20A ALA* 3.7 33.4 - - + +
23A LEU* 3.4 40.4 - - + -
24A HIS* 4.2 12.8 - - + -
28A LEU* 3.6 8.9 + - + +
29A ASN* 1.3 79.7 - - - +
31A VAL* 1.3 69.4 + - - +
32A VAL* 5.4 0.2 - - + -
225A LEU* 4.3 9.0 - - + -
228A ARG* 3.4 30.5 - - + +
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Residues in contact with VAL 31 (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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3A ASN 5.6 3.8 - - - +
4A LYS 5.6 0.7 - - - +
5A CYS* 4.0 26.0 - - + -
7A VAL 3.1 6.1 + - - +
8A VAL* 3.5 4.3 - - + -
9A VAL* 2.9 28.4 + - - +
30A VAL* 1.3 80.6 - - - +
32A VAL* 1.3 64.5 + - - +
33A LEU* 3.6 29.1 + - + -
228A ARG* 3.4 16.4 - - + +
230A LYS* 3.8 17.7 - - + -
255A TYR* 4.0 17.7 - - + -
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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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9A VAL* 3.4 9.4 - - + +
11A GLY 3.8 11.0 - - - +
12A GLY* 3.8 29.6 - - - +
16A GLY 4.7 0.9 - - - +
17A MET* 4.2 11.2 - - - -
20A ALA* 3.5 32.1 - - + -
30A VAL* 5.4 1.1 - - + -
31A VAL* 1.3 74.8 - - - +
33A LEU* 1.3 65.5 + - - +
34A GLU* 3.8 1.1 + - + +
225A LEU* 4.2 13.9 - - + -
228A ARG* 2.9 8.1 + - + +
229A VAL* 4.2 18.2 - - + -
230A LYS* 2.9 31.5 + - - +
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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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8A VAL* 3.7 27.4 - - + -
9A VAL 2.8 12.1 + - - +
10A VAL* 3.8 0.4 - - - -
11A GLY 2.9 26.3 + - - -
31A VAL* 3.6 23.1 - - + -
32A VAL* 1.3 71.3 - - - +
34A GLU* 1.3 60.5 + - - +
230A LYS* 3.8 14.1 - - + -
233A ARG* 3.9 11.9 - - + +
235A VAL* 3.7 28.7 - - + -
247A VAL* 3.8 8.5 - - + -
249A THR* 3.9 4.9 - - + -
255A TYR* 3.7 42.0 - - + -
1500A FAD 3.4 7.3 - - - -
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Residues in contact with GLU 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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12A GLY* 2.7 34.2 + - - +
32A VAL* 3.8 4.9 + - + -
33A LEU* 1.3 73.0 - - - +
35A ALA* 1.3 60.5 + - - +
36A ARG* 2.8 27.4 + - - +
38A ARG 3.2 22.7 - - - +
39A VAL* 4.7 3.1 - - + -
229A VAL* 4.9 2.2 - - + -
230A LYS 3.0 13.7 + - - +
231A LEU* 3.9 13.2 - - + -
232A GLU 3.0 11.8 + - - -
233A ARG 2.8 24.7 + - - -
1500A FAD 2.6 48.0 + - - -
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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