Contacts of the strand formed by residues 395 - 408 (chain A) in PDB entry 4GB1
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 GLN 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A ILE* 5.3 2.9 - - + +
382A LEU* 3.5 22.6 - - + +
383A ARG 3.6 6.1 - - - +
384A ILE* 4.0 13.5 - - + -
393A LYS 3.3 7.2 + - - +
394A GLU* 1.3 74.9 - - - +
396A ILE* 1.3 63.8 + - - +
397A ARG 4.0 14.4 - - - +
399A LYS* 3.6 31.9 - - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ASP* 3.7 22.7 - - - +
383A ARG* 2.9 29.9 + - + +
385A LYS* 3.9 33.4 - - + -
394A GLU* 5.2 2.2 - - + -
395A GLN* 1.3 76.3 + - - +
397A ARG* 1.3 85.4 + - + +
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LYS* 3.2 67.7 - - - +
366A TRP* 3.8 20.6 - - + -
381A ILE 4.4 0.9 - - - -
382A LEU* 3.4 3.1 - - - -
383A ARG* 2.7 43.3 + - + +
395A GLN* 4.0 6.7 - - - +
396A ILE* 1.3 104.1 - - + +
399A LYS* 1.3 61.2 + - - +
462A GLU* 3.5 34.3 + - + +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A TRP* 5.6 0.4 - - - -
371A ILE* 5.7 2.8 - - - +
380A GLU* 3.0 26.3 + - + +
381A ILE 3.5 5.4 - - - -
382A LEU* 3.6 22.9 - - + -
395A GLN* 3.6 23.0 - - - +
397A ARG* 1.3 75.1 - - - +
400A GLN* 1.3 66.7 + - - +
401A VAL* 3.8 21.9 - - - +
465A ASP* 3.7 12.4 - - - +
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY* 3.8 7.8 - - - -
97A PHE* 2.8 55.9 + - - +
366A TRP* 5.2 4.4 - - + -
380A GLU* 3.7 1.2 - - - -
381A ILE* 3.2 39.6 + - + +
399A LYS* 1.3 76.5 - - - +
401A VAL* 1.3 68.7 + - - +
402A VAL* 3.6 13.3 + - + +
456A MET* 3.8 13.3 - - - +
463A VAL* 3.6 32.0 + - - +
464A ALA 4.5 3.2 + - - +
465A ASP* 3.2 6.3 - - - +
468A TRP* 5.3 1.2 - - - -
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 3.8 13.0 - - + -
379A PHE 3.6 7.4 - - - +
380A GLU* 4.2 7.6 - - - +
399A LYS* 3.8 24.9 - - - +
400A GLN* 1.3 76.1 + - - +
402A VAL* 1.3 66.1 + - - +
403A VAL 3.5 26.0 - - - +
404A ASP* 4.1 7.6 - - + -
464A ALA 4.5 0.3 - - - +
465A ASP* 3.0 32.9 + - + +
466A TRP 3.2 25.4 + - - +
468A TRP* 5.0 0.5 - - - -
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 2.9 15.9 + - + +
381A ILE* 5.6 1.6 - - + +
400A GLN* 3.9 29.4 - - + +
401A VAL* 1.3 78.2 - - - +
403A VAL* 1.3 70.4 + - + +
432A PHE* 4.8 8.3 - - + -
434A VAL* 5.2 7.6 - - + -
454A ILE* 4.2 11.7 - - + -
456A MET* 4.0 30.3 - - + -
466A TRP 3.1 10.4 - - - +
468A TRP* 3.0 42.1 + - + -
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 3.4 6.8 - - - +
378A GLY* 3.0 6.9 - - - -
379A PHE* 2.6 46.2 + - + +
401A VAL* 3.8 3.4 - - - -
402A VAL* 1.3 92.1 - - + +
404A ASP* 1.3 60.6 + - - +
407A ASN* 3.7 35.0 - - + +
408A TRP 4.0 10.3 - - - +
409A SER* 4.5 1.6 - - - -
434A VAL* 4.8 6.7 - - + -
436A MET* 3.8 25.8 - - + -
454A ILE* 4.8 2.5 - - + -
467A SER* 3.8 5.6 - - - +
468A TRP 4.6 5.2 - - - +
469A HIS* 4.6 3.6 - - + -
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Residues in contact with ASP 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 4.1 0.4 - - - -
378A GLY* 3.4 1.2 - - - -
401A VAL* 4.1 12.1 - - + +
403A VAL* 1.3 74.6 - - - +
405A ASN* 1.3 60.2 + - - +
406A LEU* 2.8 22.1 + - + +
407A ASN* 2.6 46.7 + - - +
466A TRP 5.6 0.4 - - - -
467A SER* 3.2 30.7 + - - -
469A HIS* 4.6 2.8 + - - -
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Residues in contact with ASN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 3.7 34.3 - - + +
372A SER* 5.4 2.5 - - - +
377A SER* 4.2 15.7 + - - +
378A GLY* 4.1 10.1 - - - +
404A ASP* 1.3 72.8 - - - +
406A LEU* 1.3 79.1 + - - +
407A ASN 3.2 3.9 + - - -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ASP* 2.8 17.6 + - + +
405A ASN* 1.3 95.2 - - - +
407A ASN* 1.3 67.9 + - - +
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Residues in contact with ASN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A SER* 3.5 4.7 - - - -
378A GLY* 2.6 34.3 + - - -
403A VAL* 3.7 6.2 - - + +
404A ASP* 2.6 31.3 + - - +
405A ASN 3.2 1.4 + - - -
406A LEU* 1.3 89.3 + - - +
408A TRP* 1.3 61.3 + - - +
469A HIS* 3.1 57.3 + - + +
471A GLY 5.6 0.3 + - - -
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Residues in contact with TRP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A SER* 4.2 16.8 - - - -
376A ARG 3.6 14.6 - - - +
377A SER* 3.7 18.8 - - - -
403A VAL* 4.0 4.7 - - - +
407A ASN* 1.3 77.8 + - - +
409A SER* 1.3 61.2 + - - +
436A MET* 3.6 19.8 - - - +
437A ILE* 3.2 28.9 - - + +
438A ARG* 3.9 18.1 - - - -
442A GLU* 3.6 46.7 - - + -
443A GLU* 3.8 25.8 + - + +
470A ASP* 5.4 2.3 + - - +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A THR* 4.1 6.9 - - - +
376A ARG* 2.9 23.3 + - - +
378A GLY 2.9 33.6 + - - -
379A PHE* 4.4 3.5 - - - -
403A VAL* 4.5 4.3 - - - -
407A ASN 3.6 1.0 + - - -
408A TRP* 1.3 74.5 - - - +
410A GLY* 1.3 66.5 + - - -
434A VAL* 4.3 15.3 - - - -
435A GLU 3.0 16.0 - - - +
436A MET* 4.0 2.5 - - - +
437A ILE* 2.9 29.8 + - - +
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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