Contacts of the strand formed by residues 376 - 385 (chain G) in PDB entry 2W3S
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 LYS 376 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372G LEU* 3.7 3.0 - - - -
373G LYS* 2.7 41.5 + - + +
375G SER* 1.3 82.5 - - - +
377G ILE* 1.3 62.4 + - - +
403G GLY* 4.4 20.0 - - - +
404G GLN* 2.9 7.7 - - - +
405G ASP* 2.8 38.0 + - - +
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Residues in contact with ILE 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G LEU* 4.2 17.3 - - + -
371G THR 4.4 2.7 - - - +
372G LEU* 3.8 19.1 - - + -
376G LYS* 1.3 69.6 - - - +
378G GLU* 1.3 70.6 + - - +
379G THR 4.7 0.4 - - - +
380G ALA* 4.4 10.1 - - + -
401G LEU* 3.2 47.6 - - + +
402G ILE* 4.0 1.7 - - - +
403G GLY* 2.7 29.6 + - - -
404G GLN* 2.4 31.3 + - + +
405G ASP 3.4 19.7 - - - +
406G PHE* 3.8 19.1 - - + -
410G THR* 4.8 3.8 - - + -
411G ILE* 5.3 2.5 - - + -
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Residues in contact with GLU 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371G THR* 2.8 28.6 + - + +
372G LEU 3.9 2.0 - - - -
373G LYS* 3.2 59.5 + - + +
376G LYS 3.3 1.0 + - - -
377G ILE* 1.3 80.8 - - - +
379G THR* 1.3 72.3 + - - +
402G ILE* 3.4 23.4 - - - +
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Residues in contact with THR 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G LEU* 3.6 2.8 - - - +
371G THR* 2.7 49.2 + - - +
377G ILE* 4.7 0.7 - - - +
378G GLU* 1.3 88.0 + - - +
380G ALA* 1.3 66.8 + - - +
381G ARG* 4.1 10.8 - - + +
393G ARG* 6.3 0.4 - - - +
402G ILE* 5.0 3.1 - - + -
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Residues in contact with ALA 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370G LEU* 3.3 20.6 - - + -
377G ILE* 4.4 9.0 - - + -
378G GLU 3.8 0.2 + - - -
379G THR* 1.3 79.6 - - - +
381G ARG* 1.3 62.1 + - - +
382G ILE* 4.2 7.6 - - + -
393G ARG* 4.0 2.3 + - - -
398G GLU* 3.0 36.0 - - - +
401G LEU* 4.9 2.0 - - + -
402G ILE* 3.8 25.9 - - + +
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Residues in contact with ARG 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G ILE* 2.3 36.2 + - - +
300G ALA* 3.1 30.5 - - - +
302G GLY* 3.5 18.5 - - - -
317G PRO* 4.8 7.3 - - - +
319G GLU* 2.8 32.6 + - - -
367G CYS 4.1 0.8 - - - +
368G LEU 3.5 0.2 - - - -
369G ASN* 2.6 54.8 + - + +
379G THR* 4.1 11.3 - - + +
380G ALA* 1.3 71.3 - - - +
382G ILE* 1.3 60.5 + - - +
383G ALA 4.2 0.4 - - - -
393G ARG* 3.5 28.2 - - - +
398G GLU* 3.4 2.0 - - - -
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Residues in contact with ILE 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G ALA* 4.8 0.4 - - - +
367G CYS 3.3 4.9 - - - +
368G LEU* 3.9 28.7 - - + -
370G LEU* 3.9 23.6 - - + -
380G ALA* 4.2 6.1 - - + -
381G ARG* 1.3 77.1 - - - +
383G ALA* 1.3 59.0 + - - +
384G PHE* 3.9 18.4 - - + -
393G ARG* 3.1 6.4 - - - +
394G ALA* 2.9 47.2 + - + -
397G PHE* 4.3 19.7 - - + -
398G GLU* 2.8 37.4 + - + +
401G LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296G PRO* 3.5 25.8 - - + +
299G ILE* 4.0 27.1 - - + -
300G ALA* 4.1 5.0 - - + +
365G CYS 4.0 0.3 - - - +
367G CYS* 2.8 37.9 + - - +
382G ILE* 1.3 76.1 - - - +
384G PHE* 1.3 66.9 + - - +
392G LYS 3.3 11.4 - - - +
393G ARG* 4.4 1.6 - - + -
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Residues in contact with PHE 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296G PRO* 4.0 5.7 - - - +
364G VAL* 4.2 10.1 - - + -
365G CYS 3.4 5.4 - - - -
366G GLY* 3.4 30.1 - - - -
368G LEU* 4.8 7.9 - - + -
382G ILE* 3.9 22.0 - - + -
383G ALA* 1.3 74.7 - - - +
385G GLY* 1.3 59.3 + - - +
387G MET* 3.7 22.4 + - + +
390G VAL 4.7 0.5 - - - +
391G PRO* 3.4 9.4 - - - +
392G LYS* 2.9 30.4 + - - +
394G ALA* 4.5 1.6 - - + -
418G LEU* 3.8 23.6 - - + -
422G PHE* 3.6 27.4 - + + -
439G ALA* 3.6 39.3 - - + -
442G MET* 4.0 6.3 - - - -
443G ALA* 5.9 0.4 - - + -
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Residues in contact with GLY 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290G PRO 3.5 9.2 - - - -
291G ILE* 4.9 4.3 - - - -
296G PRO* 3.7 17.5 - - - +
362G SER* 6.0 0.4 - - - -
363G ALA 3.9 1.9 - - - +
364G VAL* 3.9 0.2 - - - -
365G CYS* 2.9 37.6 + - - +
384G PHE* 1.3 71.6 - - - +
386G GLY* 1.3 64.9 + - - -
387G MET* 3.2 13.1 + - - +
391G PRO* 5.0 0.9 - - - -
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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