Contacts of the strand formed by residues 314 - 320 (chain A) in PDB entry 1UWB
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A THR* 3.5 12.9 - - - +
270A ILE* 4.4 17.2 - - + +
271A TYR* 3.3 33.5 + - + -
272A PRO* 4.5 16.2 - - + -
309A ILE* 6.2 2.7 - - + -
312A GLU* 4.3 7.9 - - + +
313A PRO* 1.3 78.5 - - - +
315A HIS* 1.3 87.4 + - + +
348A ASN* 5.1 5.6 - - + +
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Residues in contact with HIS 315 (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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238A LYS* 3.3 47.6 + - + +
240A THR* 3.0 14.6 - - + -
270A ILE* 3.6 11.0 - - - +
313A PRO 5.2 1.4 + - - -
314A VAL* 1.3 89.8 - - + +
316A GLY* 1.3 63.3 + - - +
317A VAL* 5.3 6.6 - - + +
347A LYS* 4.9 12.0 + - - +
348A ASN* 4.1 9.2 + - - +
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Residues in contact with GLY 316 (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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238A LYS* 3.2 11.0 - - - +
239A TRP* 2.9 46.3 + - - -
240A THR* 3.4 1.2 - - - +
270A ILE* 3.5 14.3 - - - +
315A HIS* 1.3 75.6 - - - +
317A VAL* 1.3 64.9 - - - -
348A ASN 3.2 8.1 - - - -
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Residues in contact with VAL 317 (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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98A ALA 4.5 1.4 - - - +
237A ASP 4.1 9.2 - - - +
238A LYS* 6.1 0.4 - - + -
239A TRP* 3.2 18.9 + - - +
315A HIS* 5.3 7.0 - - + +
316A GLY* 1.3 74.6 - - - +
318A TYR* 1.3 66.8 + - - +
343A GLN* 6.0 1.3 - - + +
344A GLU* 4.7 8.3 - - - +
347A LYS* 3.5 57.2 - - + +
348A ASN 2.6 22.8 + - - +
349A LEU* 3.0 34.1 - - + +
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Residues in contact with TYR 318 (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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97A PRO 4.2 13.0 - - - -
98A ALA 4.6 1.3 - - - -
100A LEU* 3.7 5.8 - - + +
101A LYS 3.6 19.1 - - - -
102A LYS* 3.5 27.1 - - + +
234A LEU* 3.3 14.1 - - + +
235A HIS 2.8 29.8 + - - -
236A PRO 3.7 4.3 - - - -
237A ASP 3.6 13.3 + - - +
238A LYS 3.1 9.4 + - - -
239A TRP* 3.3 31.2 - + + -
317A VAL* 1.3 85.7 - - - +
319A TYR* 1.3 65.2 + - - +
320A ASP* 3.9 2.3 + - - +
343A GLN* 5.1 3.3 - - - +
344A GLU* 5.6 0.7 - - - +
349A LEU* 3.2 16.7 - - - +
559A TBO 3.0 34.7 - + - -
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Residues in contact with TYR 319 (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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98A ALA 4.2 0.6 + - - -
99A GLY 3.3 10.3 - - - +
100A LEU 2.5 27.3 + - - +
101A LYS* 2.9 36.1 - - + +
102A LYS* 3.7 4.9 + - - +
318A TYR* 1.3 74.1 - - - +
320A ASP* 1.3 83.7 + - - +
321A PRO* 3.4 41.0 + - + +
323A LYS 3.9 8.7 + - - -
325A LEU* 3.8 16.5 - - + +
343A GLN* 3.4 21.3 - - + -
349A LEU* 4.8 2.0 - - + -
383A TRP* 3.2 44.4 - + + +
385A LYS* 3.7 26.1 - - - +
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Residues in contact with ASP 320 (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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318A TYR 3.9 2.1 + - - +
319A TYR* 1.3 79.7 - - - +
321A PRO* 1.3 63.8 - - - +
322A SER* 2.6 44.9 + - - -
323A LYS* 3.6 8.3 - - - +
343A GLN* 2.4 36.4 + - + +
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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