Contacts of the strand formed by residues 313 - 318 (chain D) in PDB entry 2W8B
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 GLN 313 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D THR* 3.7 2.8 - - - -
306D SER 3.0 30.2 + - - +
309D ALA* 5.1 6.5 - - + -
311D ARG 3.6 8.2 - - - +
312D PRO* 1.3 77.9 - - - +
314D VAL* 1.3 61.4 + - - +
315D TYR* 3.6 17.1 - - + -
326D ARG* 3.9 28.9 + - + +
328D THR* 2.7 38.8 + - - +
331D GLY 3.3 11.4 + - - +
332D SER* 3.1 26.0 - - - +
334D ASN* 3.0 32.7 + - - +
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ALA* 3.9 12.3 - - + -
304D PHE 3.3 13.9 - - - +
313D GLN* 1.3 72.0 - - - +
315D TYR* 1.4 63.7 + - - +
326D ARG* 3.8 1.2 - - - +
327D ILE* 2.8 48.9 + - + -
328D THR* 2.9 33.2 + - + -
334D ASN* 4.0 2.9 - - + +
335D GLN* 3.9 27.6 - - - +
336D ASP 4.8 0.7 - - - +
337D ALA* 4.1 18.2 - - + -
346D MET* 4.0 8.3 - - - -
348D MET* 4.4 5.8 - - - -
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Residues in contact with TYR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA* 3.0 6.8 - - - +
304D PHE* 2.8 52.6 + + + -
306D SER* 3.6 28.5 - - - -
308D GLN* 3.7 26.0 + - + +
309D ALA* 3.5 31.1 + - - +
313D GLN* 3.6 23.6 - - + -
314D VAL* 1.4 77.8 - - - +
316D LYS* 1.3 61.9 + - - +
324D PRO* 4.1 11.0 - - + -
325D GLN* 3.1 15.5 - - - -
326D ARG* 3.3 36.7 - - + +
327D ILE* 4.1 3.1 - - - +
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D PHE* 3.6 47.6 - - + -
301D ASN* 3.9 25.7 - - - +
302D LEU 3.2 5.8 - - - +
304D PHE* 4.0 1.3 - - - -
315D TYR* 1.3 76.7 - - - +
317D VAL* 1.3 65.6 + - - +
323D ALA 4.4 0.5 - - - +
324D PRO* 3.3 2.8 - - - +
325D GLN* 2.7 54.4 + - + +
327D ILE* 3.9 26.0 - - + -
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D LEU* 4.3 7.9 - - + -
283D VAL* 3.9 29.6 - - + +
284D THR* 4.7 1.1 - - + -
301D ASN* 3.5 5.9 - - - -
302D LEU* 2.8 39.3 + - + +
304D PHE* 3.6 26.0 - - + -
316D LYS* 1.3 77.7 - - - +
318D ASN* 1.3 70.6 + - - +
319D ILE 3.8 0.3 + - - -
322D GLY 3.7 24.2 - - - +
323D ALA 4.3 2.0 - - - +
324D PRO* 3.9 19.7 - - + -
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Residues in contact with ASN 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D VAL* 4.4 1.9 - - - +
300D GLN* 3.5 15.9 + - - +
301D ASN* 3.5 25.0 + - - +
317D VAL* 1.3 85.4 - - - +
319D ILE* 1.3 65.6 + - - +
320D ASN* 2.5 58.2 + - - +
321D GLY 3.3 23.8 + - - +
322D GLY* 5.9 0.2 - - - -
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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