Contacts of the strand formed by residues 266 - 270 (chain A) in PDB entry 1XJB
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.8 25.1 - - + -
16A MET* 3.8 15.0 - - - -
17A PRO 3.6 14.4 - - - +
18A VAL* 3.4 26.7 - - + +
48A HIS* 4.1 13.2 - - + -
212A VAL* 3.6 18.4 - - + -
213A LEU 3.2 6.1 + - - -
214A VAL* 3.2 19.4 - - + +
215A ALA 2.7 27.2 + - - -
264A GLY 4.0 2.1 + - - +
265A VAL* 1.3 73.4 - - - +
267A VAL* 1.4 63.7 + - - +
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Residues in contact with VAL 267 (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 VAL 3.0 7.2 + - - +
19A LEU* 3.5 18.2 - - + +
20A GLY 2.9 21.8 + - - -
215A ALA* 4.0 3.8 - - + -
218A ALA* 3.3 30.1 - - + -
257A LEU* 3.5 26.2 - - + +
260A GLN* 3.8 24.5 - - + -
261A LEU* 3.8 22.7 - - + -
265A VAL 3.6 0.4 + - - -
266A VAL* 1.4 73.6 - - - +
268A LEU* 1.4 69.4 + - - +
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Residues in contact with LEU 268 (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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20A GLY* 3.2 27.6 - - - +
21A PHE 5.1 0.2 - - - -
22A GLY 4.8 2.0 - - - +
48A HIS* 3.9 18.4 - - + +
50A ASP* 3.8 18.6 - - + +
190A GLN* 3.7 30.5 - - - +
214A VAL* 3.9 14.8 - - + -
215A ALA 3.0 21.0 + - - +
216A TYR* 4.1 1.8 - - + -
218A ALA* 3.6 13.0 + - - +
257A LEU* 3.8 0.7 - - - +
266A VAL* 5.4 0.4 - - + -
267A VAL* 1.4 88.6 - - - +
269A ALA* 1.3 64.7 + - - +
1001A NAP 3.5 36.6 + - - +
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Residues in contact with ALA 269 (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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19A LEU* 4.5 7.9 - - + -
20A GLY 2.9 8.7 + - - +
21A PHE* 3.6 14.0 - - - -
22A GLY* 3.0 16.6 + - - +
46A PHE* 4.4 3.4 - - + -
219A LEU* 4.4 5.6 - - + -
257A LEU* 3.9 23.6 - - + -
268A LEU* 1.3 79.0 - - - +
270A LYS* 1.3 61.6 + - - +
280A ASN* 4.0 23.2 + - + +
1001A NAP 3.7 6.1 - - - -
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Residues in contact with LYS 270 (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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22A GLY 3.4 19.3 - - - +
24A TYR 3.4 26.7 - - - +
25A ALA* 4.4 7.3 - - - +
26A PRO* 5.1 6.2 - - - +
29A VAL* 6.1 1.4 - - - +
222A HIS* 6.1 2.4 - - + +
269A ALA* 1.3 74.4 - - - +
271A SER* 1.3 62.4 + - - +
272A TYR* 3.5 35.1 - - + +
1001A NAP 2.7 114.6 + - + +
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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