Contacts of the strand formed by residues 303 - 307 (chain A) in PDB entry 5X61
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 ILE 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A VAL* 3.9 28.3 - - + -
261A VAL 3.6 5.8 - - - +
262A ALA* 3.8 16.2 - - + -
263A PRO* 3.8 9.9 - - + -
267A PRO* 4.0 9.4 - - + -
270A ALA* 4.8 1.3 - - + -
271A ALA 3.1 14.6 + - - +
272A VAL* 3.3 9.8 - - + +
273A MET 2.9 25.2 + - - -
302A VAL* 1.3 68.3 - - - +
304A VAL* 1.3 62.1 + - - +
305A VAL* 4.2 2.7 - - + -
344A ILE* 4.0 18.4 - - + -
347A PHE* 3.4 25.1 - - + +
348A GLY 3.8 20.2 - - - +
349A GLY* 3.9 9.2 - - - -
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN 4.0 0.5 - - - +
260A VAL* 3.8 0.7 - - - -
261A VAL* 2.9 37.3 + - + +
273A MET* 3.4 11.0 - - + +
275A TRP* 5.5 0.7 - - + -
293A HIS* 3.9 42.3 - - + +
296A LEU* 3.8 27.8 - - + -
297A ALA* 3.7 27.8 - - + +
302A VAL* 3.2 12.1 + - + +
303A ILE* 1.3 72.2 - - - +
305A VAL* 1.3 65.4 + - - +
357A PHE* 5.2 2.9 - - + -
608A PHE* 4.8 5.2 - - + -
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 3.7 19.3 - - + -
259A ASN 3.3 9.6 - - - +
260A VAL* 4.2 8.7 - - + -
272A VAL* 3.9 15.0 - - + -
273A MET 2.9 8.2 + - - +
274A LEU* 3.2 22.4 - - + -
275A TRP* 2.6 34.8 + - - +
293A HIS* 4.6 1.6 - - - -
303A ILE* 4.2 4.9 - - + -
304A VAL* 1.3 80.0 - - - +
306A SER* 1.3 60.6 + - - +
307A LEU* 5.9 0.4 - - + -
340A VAL* 4.0 13.5 - - + -
344A ILE* 3.6 29.4 - - + -
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Residues in contact with SER 306 (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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257A TYR 4.4 0.2 - - - +
258A ILE* 3.4 6.4 - - - +
259A ASN* 2.9 51.8 + - - +
274A LEU* 5.0 0.9 - - - -
275A TRP* 3.6 17.7 - - - -
286A ALA* 3.7 13.3 - - - +
293A HIS* 2.6 37.0 + - - -
305A VAL* 1.3 76.0 - - - +
307A LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 307 (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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196A TYR* 4.2 4.0 - - + +
257A TYR 3.8 4.5 - - - -
258A ILE* 4.2 8.1 - - + -
259A ASN* 5.8 0.2 - - - +
274A LEU* 3.6 28.3 - - + -
275A TRP 3.8 6.6 + - - +
276A ILE* 4.2 15.3 - - + -
277A PHE* 3.6 14.4 + - - -
286A ALA* 3.5 13.5 - - - +
305A VAL* 5.9 0.4 - - + -
306A SER* 1.3 75.8 - - - +
308A GLN* 1.3 79.9 + - - +
309A TYR* 3.8 19.9 - - + +
333A GLN* 3.9 26.9 - - + +
336A ALA* 3.8 26.0 - - + -
337A LEU* 4.8 3.6 - - + -
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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