Contacts of the strand formed by residues 312 - 317 (chain Y) in PDB entry 1WWA
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 SER 312 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310Y ALA 4.1 0.2 + - - -
311Y PRO* 1.3 73.6 - - - +
313Y LEU* 1.3 63.7 + - - +
314Y ARG* 5.2 8.1 + - - -
362Y LEU 3.5 0.9 - - - +
363Y ALA* 3.1 6.9 - - - -
364Y ALA* 2.8 40.1 + - - +
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Residues in contact with LEU 313 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303Y PHE* 4.5 12.6 - - + -
305Y VAL* 3.6 33.0 - - + -
311Y PRO 4.3 5.6 - - - +
312Y SER* 1.3 83.0 - - - +
314Y ARG* 1.3 72.9 + - - +
315Y TRP* 5.3 5.2 - - + +
330Y THR* 4.6 9.2 - - + +
332Y PHE* 3.8 33.4 - - + -
342Y ARG* 4.7 4.0 - - - +
361Y LEU* 4.2 13.9 - - + -
362Y LEU 3.2 5.2 - - - +
363Y ALA* 4.0 11.7 - - + -
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Residues in contact with ARG 314 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312Y SER* 5.2 8.5 + - - -
313Y LEU* 1.3 82.9 - - - +
315Y TRP* 1.3 68.9 + - - +
316Y LEU* 5.3 1.5 - - + +
321Y VAL* 5.3 10.5 - - + -
360Y THR 3.7 0.2 - - - +
361Y LEU* 3.3 5.9 - - - +
362Y LEU* 2.8 70.1 + - + +
363Y ALA 5.8 0.2 - - - -
364Y ALA* 4.9 15.2 - - - +
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Residues in contact with TRP 315 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290X LEU* 3.9 31.0 - - + -
301Y ILE* 4.4 10.1 - - + -
303Y PHE* 3.7 24.9 - + - -
313Y LEU* 5.3 4.7 - - + +
314Y ARG* 1.3 79.0 - - - +
316Y LEU* 1.3 76.6 + - - +
321Y VAL* 3.7 5.8 - - - +
322Y LEU* 3.1 43.5 + - + +
324Y GLU* 3.9 13.5 - - + -
330Y THR* 3.1 27.1 + - - +
346Y LEU* 3.5 45.2 - - + +
359Y TYR* 4.5 8.7 - + + -
360Y THR 3.1 24.7 - - - -
361Y LEU* 3.8 27.5 - - + +
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Residues in contact with LEU 316 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314Y ARG* 5.3 2.7 - - + +
315Y TRP* 1.3 94.3 - - - +
317Y PHE* 1.3 61.4 + - - +
318Y ASN 3.9 0.2 - - - -
319Y GLY* 3.8 26.2 - - - +
320Y SER 3.1 6.5 - - - +
321Y VAL* 3.5 23.6 - - + +
322Y LEU* 4.0 3.1 - - - +
358Y ASN 3.6 0.9 - - - +
359Y TYR* 3.4 8.3 - - - +
360Y THR* 2.8 49.8 + - + +
362Y LEU* 3.6 31.2 - - + -
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Residues in contact with PHE 317 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316Y LEU* 1.3 73.2 - - - +
318Y ASN* 1.3 89.4 + - + +
319Y GLY 3.2 0.7 - - - -
320Y SER* 2.7 24.8 + - - +
321Y VAL 5.4 0.9 - - - +
322Y LEU* 3.7 27.3 - - + +
354Y VAL 3.7 13.0 - - - -
355Y ASN* 3.1 30.7 - - - -
356Y ASN 3.2 20.4 - - - -
357Y GLY* 3.5 17.7 - - - -
358Y ASN 3.6 2.2 - - - -
359Y TYR* 3.3 26.0 - + + -
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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