Contacts of the strand formed by residues 324 - 328 (chain A) in PDB entry 1XAH
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LYS* 2.7 29.8 - - + +
237A PHE* 3.7 18.8 - - + +
239A ASN* 3.9 16.2 - - + +
240A LEU* 3.3 34.8 - - + +
241A GLY 4.4 2.1 + - - +
243A THR* 4.2 3.8 + - - -
267A GLN* 3.4 9.2 - - - +
323A MET* 1.3 74.1 - - - +
325A LEU* 1.3 59.7 + - - +
332A ILE* 3.5 29.8 - - + -
333A VAL 3.4 4.9 - - - +
334A VAL* 4.2 11.9 - - + -
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Residues in contact with LEU 325 (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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240A LEU* 4.9 0.4 - - - -
267A GLN* 3.7 20.4 - - + +
270A VAL* 3.7 12.1 - - + -
271A ALA* 4.5 5.6 - - + -
274A LEU* 3.6 30.7 - - + -
275A PHE* 3.8 19.1 - - + -
323A MET* 3.4 43.1 - - + +
324A VAL* 1.3 78.6 - - - +
326A MET* 1.3 59.8 + - - +
327A ARG 3.6 1.1 + - - -
332A ILE* 3.4 4.2 - - - +
333A VAL* 2.7 50.5 + - + +
335A GLN* 4.7 6.3 - - + -
337A VAL* 4.4 7.4 - - + -
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Residues in contact with MET 326 (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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184A LEU* 3.0 42.0 - - + +
185A LEU* 4.4 3.4 - - + +
240A LEU* 4.6 6.9 - - + +
267A GLN* 2.9 21.4 + - - +
268A PHE* 4.0 22.7 - - + -
271A ALA* 3.4 10.7 - - - +
279A HIS* 3.1 22.6 + - + -
325A LEU* 1.3 72.0 - - - +
327A ARG* 1.3 60.4 + - - +
328A GLN* 3.5 20.0 - - - +
329A PHE* 3.8 33.9 - - + -
331A ASP 4.0 2.5 - - - -
332A ILE* 3.9 27.4 - - + +
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Residues in contact with ARG 327 (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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275A PHE* 3.2 57.2 - - + -
277A SER* 3.2 25.9 + - - +
279A HIS* 4.1 1.2 + - - -
325A LEU 3.6 2.8 + - - -
326A MET* 1.3 73.7 - - - +
328A GLN* 1.3 63.4 + - + +
331A ASP* 2.9 35.8 + - - +
333A VAL* 3.1 32.9 - - + +
335A GLN* 4.8 4.2 + - - -
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Residues in contact with GLN 328 (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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279A HIS* 4.8 6.1 - - - -
326A MET* 3.2 12.6 - - - +
327A ARG* 1.3 84.0 - - + +
329A PHE* 1.3 72.9 + - + +
330A GLY 2.9 0.5 + - - -
331A ASP* 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