Contacts of the strand formed by residues 405 - 411 (chain B) in PDB entry 2WNW
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 ARG 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 3.5 29.5 + - + +
39B ARG* 5.3 0.4 - - - +
384B MET* 4.1 5.6 - - + -
398B PHE 3.5 4.3 - - - -
399B VAL* 3.7 19.2 - - + +
403B GLY* 2.9 23.1 + - - -
404B GLU* 1.3 74.6 - - - +
406B VAL* 1.3 63.2 + - - +
440B LEU 3.6 0.3 - - - +
441B LEU* 3.4 5.9 - - - -
442B TRP* 2.7 83.1 + - + +
444B GLN* 3.3 31.9 + - - +
1447B PO4 2.8 39.8 + - - -
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS 5.3 0.2 - - - +
376B TYR* 4.0 7.9 - - + +
377B VAL* 3.9 24.2 - - + -
384B MET* 3.7 2.5 - - - +
397B GLY* 3.1 2.8 - - - -
398B PHE* 2.7 47.8 + - + +
400B ASN* 3.7 28.3 - - - +
404B GLU* 4.3 5.6 - - - +
405B ARG* 1.3 80.1 - - - +
407B LEU* 1.3 65.1 + - - +
408B VAL* 4.7 2.9 - - + -
439B THR* 3.7 25.6 - - + -
440B LEU 3.3 2.7 - - - -
441B LEU* 3.6 17.0 - - + -
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.2 6.3 - - + -
36B VAL* 4.1 17.9 - - + -
384B MET* 5.1 0.7 - - + -
386B SER* 4.8 0.2 - - - +
395B GLU* 3.7 22.4 - - + +
396B VAL 3.7 17.9 - - - +
397B GLY* 3.9 6.5 - - - +
406B VAL* 1.3 75.3 - - - +
408B VAL* 1.3 64.3 + - - +
409B VAL* 3.8 18.4 - - + +
421B VAL* 3.7 42.0 - - + -
438B SER 3.6 1.4 - - - +
439B THR* 3.2 4.3 - - - -
440B LEU* 2.8 43.8 + - + +
442B TRP* 3.8 16.4 - - + -
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LEU* 5.1 4.0 - - + -
318B ILE* 4.5 10.5 - - + +
372B HIS* 3.6 28.9 - - + +
373B PHE* 3.9 45.1 - - + -
394B GLU 4.5 0.2 - - - -
395B GLU* 3.1 7.6 - - - +
396B VAL* 2.9 37.3 + - + +
398B PHE* 4.7 6.1 - - + -
406B VAL* 4.7 4.5 - - + -
407B LEU* 1.3 77.4 - - - +
409B VAL* 1.3 67.7 + - - +
410B TYR* 5.6 0.4 - - + -
437B ALA* 5.7 1.1 - - + -
438B SER 3.4 6.7 - - - +
439B THR* 4.0 10.5 - - + +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.9 27.6 - - + -
393B LEU* 4.6 10.1 - - + -
394B GLU 3.3 7.9 - - - +
395B GLU* 4.2 2.0 - - + -
407B LEU* 3.8 27.1 - - + +
408B VAL* 1.3 81.8 - - - +
410B TYR* 1.3 67.0 + - - +
419B CYS* 4.6 2.2 - - - -
421B VAL* 5.1 0.4 - - + -
430B LEU* 4.9 13.0 - - + -
432B LEU* 3.7 25.0 - - + +
437B ALA* 3.2 5.7 - - - +
438B SER* 2.9 39.6 + - - +
440B LEU* 6.3 0.7 - - + -
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Residues in contact with TYR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B TRP* 3.7 10.8 - + - -
311B HIS* 2.7 47.6 + + - +
314B LEU* 3.9 27.1 - - + -
315B HIS 4.5 7.0 - - - -
318B ILE* 3.5 19.1 - - + -
392B LEU 3.4 2.6 - - - +
393B LEU* 3.6 1.6 - - - -
394B GLU* 2.7 64.9 + - - +
408B VAL* 5.6 0.4 - - + -
409B VAL* 1.3 76.4 - - - +
411B ASN* 1.3 61.5 + - - +
412B ARG* 3.6 21.2 + - + +
432B LEU* 4.5 1.3 - - - -
435B SER* 3.5 33.5 + - - -
436B GLY 3.5 9.9 - - - -
437B ALA* 4.7 2.0 - - + -
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B LEU 3.9 3.4 - - - +
393B LEU* 3.7 16.2 - - + +
410B TYR* 1.3 70.8 - - - +
412B ARG* 1.3 57.5 + - - +
413B ASP* 3.0 24.0 + - - +
415B GLN 3.1 24.9 + - - -
417B ARG* 3.4 15.4 - - - +
432B LEU* 3.3 27.8 + - + +
433B PRO 3.1 21.3 + - - +
434B PRO* 3.9 2.2 - - - +
435B SER* 2.8 34.8 + - - -
436B GLY 2.9 10.0 + - - +
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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