Contacts of the strand formed by residues 395 - 400 (chain X) in PDB entry 2QW0
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 395 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X LEU* 3.9 32.3 - - + -
322X THR 3.4 2.8 - - - +
323X GLU* 3.2 3.0 - - - -
324X MET* 2.7 44.7 + - - +
326X PRO* 5.0 0.4 - - + -
332X VAL* 4.6 5.2 - - + -
334X ILE* 4.3 6.7 - - + -
353X LEU* 4.5 6.5 - - + -
387X ALA* 3.7 25.4 - - + -
388X VAL 3.7 2.9 - - - -
389X TRP* 3.5 38.3 - - + -
394X THR* 1.3 70.1 - - - +
396X ARG* 1.3 62.5 + - - +
397X ILE* 3.8 5.5 + - + +
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Residues in contact with ARG 396 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322X THR* 3.5 16.8 - - - +
323X GLU* 2.6 42.3 + - - +
387X ALA* 3.1 6.5 - - - -
388X VAL* 2.8 59.6 + - + +
390X THR* 3.6 31.6 - - + +
391X PRO* 5.0 5.5 - - - +
392X GLU* 5.0 2.0 + - - -
394X THR 3.7 1.2 + - - -
395X VAL* 1.3 69.9 - - - +
397X ILE* 1.3 65.6 + - - +
398X LEU* 3.6 20.9 + - + +
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Residues in contact with ILE 397 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282X ALA* 4.4 18.8 - - + -
304X TYR* 3.8 27.4 - - + -
313X LEU* 4.0 14.8 - - + -
322X THR* 2.9 40.2 + - + +
324X MET* 4.7 7.0 - - + -
353X LEU* 3.7 30.7 - - + -
385X ASP* 4.9 11.4 - - + +
386X VAL 3.7 5.4 - - - +
387X ALA* 4.4 4.7 - - + -
395X VAL* 4.2 7.0 - - + +
396X ARG* 1.3 72.5 - - - +
398X LEU* 1.3 63.3 + - - +
399X GLY* 4.2 10.1 - - - +
419X ARG* 5.2 1.4 + - - -
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Residues in contact with LEU 398 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X GLU* 3.3 44.6 - - + +
386X VAL* 2.7 27.1 + - + +
387X ALA 4.0 10.1 - - - -
388X VAL* 4.1 9.2 - - + +
396X ARG* 3.9 32.1 - - + +
397X ILE* 1.3 75.6 - - - +
399X GLY* 1.3 54.7 + - - +
413X HIS* 3.6 36.3 - - + +
415X SER* 3.1 16.6 + - - -
416X GLU* 5.2 0.9 + - - +
419X ARG* 4.7 6.3 + - - +
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Residues in contact with GLY 399 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X ASP* 3.6 6.7 - - - +
386X VAL* 2.7 33.2 + - - +
397X ILE* 3.7 7.3 - - - +
398X LEU* 1.3 79.7 - - - +
400X ARG* 1.3 60.7 + - - +
413X HIS* 4.5 4.9 - - - -
415X SER* 4.0 9.9 - - - -
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Residues in contact with ARG 400 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283X THR* 5.9 5.3 - - - +
384X SER* 3.6 7.9 - - - +
385X ASP* 3.5 15.9 - - - +
386X VAL* 4.3 1.8 - - - +
399X GLY* 1.3 75.2 - - - -
401X VAL* 1.3 66.2 + - - +
402X ASP* 4.0 12.1 - - + +
403X ASP* 2.3 61.2 + - - +
404X MET* 3.4 12.1 + - - +
413X HIS* 4.8 1.4 + - - -
492X LYS* 4.3 29.9 - - - +
495X ARG* 4.3 11.7 - - - +
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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