Contacts of the strand formed by residues 429 - 439 (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 VAL 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A CYS* 3.7 6.1 - - + -
416A THR* 3.3 6.7 - - - -
417A LEU* 3.2 58.8 + - + -
423A SER* 4.2 12.8 - - - +
425A LYS* 3.6 35.4 - - + +
427A CYS 3.5 1.0 + - - +
428A LEU* 1.3 69.4 - - - +
430A PRO* 1.3 77.1 - - + +
431A CYS* 3.5 4.0 + - - -
457A CYS* 4.4 1.8 - - + -
458A GLY 3.5 25.4 - - - +
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Residues in contact with PRO 430 (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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91A ILE* 3.9 7.0 - - + -
92A CYS* 3.6 28.5 - - + +
94A ALA* 4.4 7.4 - - + -
97A PHE* 3.8 10.1 - - + -
359A PHE* 3.5 41.1 - - + -
361A GLN* 5.1 3.1 - - - +
366A TRP* 6.1 0.2 - - + -
415A PHE 4.2 0.7 - - - +
416A THR* 4.6 2.0 - - + -
428A LEU 3.2 9.8 - - - +
429A VAL* 1.3 85.8 - - + +
431A CYS* 1.3 56.7 + - - +
458A GLY* 2.7 44.1 + - - +
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Residues in contact with CYS 431 (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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97A PHE* 4.8 1.3 - - - -
359A PHE* 3.2 11.3 - - - -
415A PHE* 2.8 54.2 + - + +
417A LEU* 3.7 23.8 - - - -
429A VAL* 3.9 3.8 - - - -
430A PRO* 1.3 77.8 - - - +
432A PHE* 1.3 62.0 + - - +
456A MET 3.2 5.4 - - - +
457A CYS* 2.0 49.1 - - - -
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Residues in contact with PHE 432 (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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97A PHE* 3.5 41.1 - + + -
357A PHE* 3.4 36.8 - + + -
359A PHE* 4.8 0.2 - + - -
379A PHE* 4.0 11.7 - + - -
381A ILE* 3.8 16.4 - - + -
402A VAL* 4.8 10.5 - - + -
413A GLY 3.1 17.0 - - - +
415A PHE* 4.2 3.1 - - - -
431A CYS* 1.3 76.1 - - - +
433A TRP* 1.3 62.0 + - - +
434A VAL* 3.5 29.2 - - + -
455A VAL* 3.3 7.9 - - - +
456A MET* 2.8 61.6 + - + -
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Residues in contact with TRP 433 (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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119A GLU 5.0 0.7 - - - -
120A PRO* 4.0 16.8 - - + +
121A PHE* 3.3 34.8 - - + +
122A VAL* 3.6 39.4 + - + +
229A GLU 3.5 15.3 - - - -
230A SER* 4.4 2.4 + - - -
355A LYS* 3.9 4.5 - - + -
411A TYR* 3.6 37.9 - + + -
412A SER* 3.2 35.3 - - - -
413A GLY* 3.2 35.5 + - - -
414A SER 4.1 1.8 + - - +
415A PHE* 4.1 6.7 - + - -
432A PHE* 1.3 77.8 - - - +
434A VAL* 1.3 68.0 + - - +
435A GLU* 3.7 15.3 - - + -
453A SER* 5.4 3.8 - - - -
454A ILE 3.4 9.4 - - - +
455A VAL* 4.1 5.4 - - + -
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Residues in contact with VAL 434 (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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379A PHE* 3.7 38.1 - - + -
402A VAL* 5.2 5.4 - - + -
403A VAL* 4.8 3.8 - - + -
409A SER* 4.3 8.3 - - - -
410A GLY 4.9 0.2 - - - +
411A TYR 3.5 3.6 - - - +
412A SER* 3.7 11.0 - - - +
432A PHE* 3.5 27.6 - - + -
433A TRP* 1.3 81.7 - - - +
435A GLU* 1.3 72.5 + - - +
436A MET* 3.9 8.1 - - + +
453A SER* 3.4 4.2 - - - -
454A ILE* 3.0 39.9 + - + +
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Residues in contact with GLU 435 (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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118A ARG* 2.6 46.3 + - - -
119A GLU 2.9 15.0 + - - -
120A PRO* 3.5 20.2 - - + -
409A SER* 3.0 21.7 - - - -
410A GLY* 3.2 4.2 + - - -
411A TYR* 2.8 40.3 + - + +
433A TRP* 3.7 5.7 - - + -
434A VAL* 1.3 76.1 - - - +
436A MET* 1.3 64.5 + - - +
437A ILE* 3.6 9.6 - - + +
451A SER* 3.0 21.2 + - - +
452A SER 3.6 4.3 - - - -
453A SER* 4.5 2.0 - - - +
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Residues in contact with MET 436 (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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102A LYS* 4.3 3.4 - - - -
403A VAL* 3.8 19.1 - - + -
408A TRP 3.6 17.0 - - - +
409A SER* 3.5 6.1 - - - -
434A VAL* 3.9 5.8 - - + +
435A GLU* 1.3 80.8 - - - +
437A ILE* 1.3 61.0 + - - +
438A ARG* 3.7 7.2 + - - +
451A SER* 3.1 4.6 - - - -
452A SER* 2.7 47.2 + - - +
453A SER 3.8 13.5 - - - +
454A ILE* 3.5 19.5 - - + -
468A TRP 3.4 27.6 - - - +
469A HIS* 3.7 6.5 - - - -
470A ASP* 3.6 26.9 - - + +
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Residues in contact with ILE 437 (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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118A ARG* 3.3 33.9 - - - +
376A ARG* 4.4 16.4 - - + +
408A TRP* 3.2 28.1 - - + +
409A SER 2.9 19.3 + - - +
410A GLY* 4.3 7.4 - - - -
411A TYR 4.9 0.2 - - - +
435A GLU* 3.6 23.1 - - - +
436A MET* 1.3 69.9 - - - +
438A ARG* 1.3 65.8 + - - +
440A LYS 4.4 6.5 - - - +
441A PRO* 5.3 4.7 - - + -
443A GLU* 3.9 1.0 - - - +
449A THR* 3.9 21.1 - - + -
450A SER 3.5 11.2 - - - +
451A SER* 4.1 1.6 - - - -
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Residues in contact with ARG 438 (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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106A ILE* 3.8 22.2 - - + -
408A TRP* 3.9 15.3 - - - +
436A MET* 4.1 2.7 - - - +
437A ILE* 1.3 82.9 - - - +
439A GLY* 1.3 62.2 + - - +
443A GLU* 2.6 37.7 + - - -
448A TRP* 3.8 6.0 - - + -
449A THR* 3.6 5.5 - - - +
450A SER 2.9 29.7 + - - +
470A ASP* 2.9 52.2 + - - +
471A GLY 3.8 6.5 - - - +
472A ALA* 3.1 32.0 + - - +
474A LEU* 3.4 21.4 - - + +
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Residues in contact with GLY 439 (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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437A ILE* 5.8 0.2 - - - +
438A ARG* 1.3 72.4 - - - +
440A LYS* 1.3 66.9 + - - +
442A GLU* 3.4 2.9 + - - +
443A GLU* 2.5 48.2 + - - +
446A THR* 3.0 19.5 - - - -
448A TRP* 3.4 6.1 - - - -
474A LEU* 3.5 6.3 - - - +
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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