Contacts of the strand formed by residues 312 - 316 (chain D) in PDB entry 6WNX
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 312 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D VAL* 4.0 11.2 - - + -
305D SER 3.1 12.1 - - - +
311D THR* 1.3 75.0 - - - +
313D ARG* 1.3 65.0 + - - +
314D LEU* 4.2 2.5 - - + -
324D ARG 4.0 0.2 - - - +
325D VAL* 3.5 4.0 - - - +
326D LEU* 2.7 59.0 + - + +
329D HIS* 4.1 5.8 - - + -
333D VAL* 3.8 14.1 - - + -
336D ILE* 3.6 23.1 - - + -
343D ILE* 4.9 1.8 - - + -
345D SER* 3.5 33.9 - - - +
355D TRP* 3.7 26.9 - - + +
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Residues in contact with ARG 313 (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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287D ASN 4.5 0.4 + - - -
288D GLY* 3.5 30.1 + - - -
289D HIS* 3.6 29.0 + - + +
290D LYS* 6.0 0.8 - - - +
304D VAL* 3.3 4.3 - - - -
305D SER* 2.9 32.2 + - - -
309D ASP* 5.5 0.4 + - - -
311D THR* 4.5 6.1 + - - +
312D ILE* 1.3 76.8 - - - +
314D LEU* 1.3 64.8 + - - +
315D TRP* 3.4 48.6 - - + +
322D CYS* 3.6 32.8 - - - +
324D ARG 3.4 2.5 - - - -
325D VAL* 4.0 21.5 - - + +
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D LEU* 4.2 7.6 - - + -
303D VAL 3.5 4.3 - - - -
304D VAL* 3.8 13.7 - - + -
312D ILE* 4.2 3.4 - - + -
313D ARG* 1.3 79.1 - - - +
315D TRP* 1.3 56.4 + - - +
322D CYS* 3.4 6.2 - - - -
323D LEU* 2.7 35.5 + - + -
324D ARG* 2.9 28.3 + - + +
326D LEU* 3.9 27.4 - - + -
343D ILE* 4.0 9.2 - - + -
357D LEU* 4.1 11.9 - - + -
360D ALA* 3.7 24.5 - - + -
361D LEU* 3.7 25.4 - - + -
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Residues in contact with TRP 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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272D ILE* 3.4 13.9 - - + +
286D LEU* 3.6 34.8 - - + -
287D ASN 3.3 35.2 - - - -
288D GLY 3.9 1.1 - - - -
289D HIS* 3.9 14.1 - + - -
301D ARG 3.5 0.2 - - - +
302D LEU* 3.4 10.6 - - - +
303D VAL* 2.7 54.7 + - + +
305D SER* 2.9 20.8 + - - -
313D ARG* 3.4 48.2 - - + +
314D LEU* 1.3 77.7 - - - +
316D ASP* 1.3 59.5 + - - +
317D ILE 3.9 0.2 - - - -
320D GLY 3.4 23.3 - - - -
321D ALA 3.3 6.1 - - - +
322D CYS* 4.0 13.7 - - + -
323D LEU* 3.9 5.6 - - - -
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Residues in contact with ASP 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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301D ARG* 2.7 57.3 + - - +
315D TRP* 1.3 73.9 - - - +
317D ILE* 1.3 59.3 + - - +
318D GLU 3.2 1.6 + - - -
319D CYS* 3.0 40.0 + - - -
320D GLY* 2.8 31.4 + - - -
321D ALA 3.0 9.2 + - - +
323D LEU* 3.9 20.9 - - + +
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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