Contacts of the strand formed by residues 427 - 437 (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 427 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421X LEU* 3.7 23.8 - - + +
422X GLY* 4.2 17.7 - - - +
424X ALA* 3.0 20.1 + - + +
426X GLY* 1.3 79.0 - - - +
428X THR* 1.3 61.7 + - - +
429X GLU 3.9 25.8 - - - +
430X VAL* 4.4 6.5 - - + -
448X VAL* 4.8 6.1 - - + -
449X VAL 3.9 3.4 - - - +
451X ARG* 3.2 18.2 + - - +
456X LEU* 4.1 13.0 - - + -
461X LEU* 3.9 27.4 - - + -
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Residues in contact with THR 428 (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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426X GLY 3.8 2.0 + - - -
427X VAL* 1.3 75.9 - - - +
429X GLU* 1.3 67.1 + - + +
449X VAL* 2.8 35.1 + - + +
450X PRO 3.5 14.4 - - - +
451X ARG* 3.8 22.5 - - - +
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Residues in contact with GLU 429 (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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427X VAL* 3.9 5.1 - - - +
428X THR* 1.3 87.1 - - + +
430X VAL* 1.3 62.5 + - - +
431X VAL* 5.4 0.5 - - - +
447X CYS 3.9 0.2 - - - +
448X VAL* 3.4 2.9 - - - -
449X VAL* 2.8 43.6 + - + +
484X GLN* 5.3 0.7 - - - -
485X LEU* 3.6 30.9 + - + +
487X LYS* 3.3 38.6 + - - +
493X VAL* 4.6 4.3 - - - +
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Residues in contact with VAL 430 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418X GLU* 3.4 40.4 - - + +
421X LEU* 3.7 29.6 - - + -
422X GLY* 3.8 19.3 - - - +
427X VAL* 4.4 2.7 - - + -
429X GLU* 1.3 77.5 - - - +
431X VAL* 1.3 79.5 + - - +
432X VAL* 4.1 6.5 - - + -
446X ALA* 4.5 1.3 - - + -
447X CYS 3.3 11.9 - - - +
448X VAL* 3.7 13.0 - - + -
485X LEU* 4.7 0.2 - - - -
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Residues in contact with VAL 431 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418X GLU* 3.6 3.4 - - - +
429X GLU* 5.4 0.2 - - - +
430X VAL* 1.3 78.9 - - - +
432X VAL* 1.3 68.2 + - - +
433X ILE* 4.2 2.4 - - + +
445X THR 4.0 0.7 - - - +
446X ALA* 3.8 0.2 - - - -
447X CYS* 2.9 37.2 + - - +
485X LEU* 3.4 24.8 - - + +
493X VAL* 3.7 23.3 - - + -
495X ARG* 3.5 41.5 - - + +
498X LEU* 4.2 20.4 - - + -
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Residues in contact with VAL 432 (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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405X ILE* 4.0 11.0 - - + -
414X PRO* 3.1 33.6 - - + +
417X ILE* 3.8 29.4 - - + -
418X GLU* 2.8 22.6 + - + +
421X LEU* 4.1 15.5 - - + -
430X VAL* 4.1 1.6 - - + -
431X VAL* 1.3 78.3 - - - +
433X ILE* 1.3 64.1 + - - +
444X VAL* 3.7 26.2 - - + -
445X THR 3.4 10.8 - - - +
446X ALA* 4.2 5.8 - - + -
495X ARG* 3.1 12.0 + - - -
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Residues in contact with ILE 433 (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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405X ILE* 3.2 12.0 - - - +
431X VAL* 4.2 15.0 - - + -
432X VAL* 1.3 78.6 - - - +
434X GLY* 1.3 59.3 + - - +
435X LEU* 3.9 19.7 - - + -
443X SER 3.5 0.2 - - - +
445X THR* 2.8 43.2 + - + +
447X CYS* 4.0 23.6 - - - -
495X ARG* 4.3 18.2 - - + +
498X LEU* 4.3 6.7 - - + -
499X VAL* 3.9 34.5 - - + +
502X VAL* 4.0 12.1 - - + -
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Residues in contact with GLY 434 (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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405X ILE* 3.3 30.3 - - - +
433X ILE* 1.3 72.7 - - - +
435X LEU* 1.3 67.1 + - - +
436X ALA 3.8 1.0 + - - -
442X GLN* 3.8 16.1 + - - +
443X SER 3.3 7.2 - - - -
499X VAL* 4.5 11.6 - - - +
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Residues in contact with LEU 435 (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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433X ILE* 3.9 22.4 + - + -
434X GLY* 1.3 73.3 - - - +
436X ALA* 1.3 63.5 + - - +
437X ASP* 2.8 17.4 + - + +
442X GLN* 3.1 5.0 - - - -
443X SER* 3.0 29.6 + - - +
445X THR* 3.6 22.7 - - + +
478X ARG* 4.6 13.7 - - - +
480X PHE* 4.3 20.9 - - + -
499X VAL* 3.9 22.9 - - + +
502X VAL* 4.3 9.6 - - + +
503X SER* 4.4 20.4 - - - -
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Residues in contact with ALA 436 (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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434X GLY 3.8 2.4 + - - -
435X LEU* 1.3 70.5 - - - +
437X ASP* 1.3 62.4 + - - +
441X GLY 4.1 6.1 - - - -
442X GLN* 4.9 1.8 - - - +
499X VAL* 5.3 5.5 - - + +
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Residues in contact with ASP 437 (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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435X LEU* 2.8 19.2 + - + +
436X ALA* 1.3 76.1 - - - +
438X GLN* 1.3 67.6 + - + +
440X TRP* 3.2 28.5 - - - -
441X GLY 3.3 19.1 + - - +
442X GLN 4.4 0.2 - - - -
443X SER* 4.2 12.3 - - - -
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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