Contacts of the strand formed by residues 449 - 459 (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 THR 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A VAL* 3.1 21.3 - - - +
118A ARG* 4.3 6.5 - - - +
136A GLN* 3.2 11.6 + - - +
145A SER 4.6 1.6 + - - -
147A GLY* 5.4 3.0 - - - -
437A ILE* 3.9 15.5 - - + -
438A ARG 3.6 8.3 - - - +
440A LYS* 2.8 42.9 + - - +
441A PRO* 5.4 0.2 - - + -
448A TRP* 1.3 84.2 + - - +
450A SER* 1.3 65.4 + - - +
501A 0LP 4.0 28.5 - - + -
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Residues in contact with SER 450 (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* 3.7 17.9 - - - +
115A PHE 4.3 2.1 + - - -
116A VAL* 3.8 2.9 - - - -
117A ILE* 2.9 40.4 + - - +
118A ARG* 4.6 1.6 - - - +
140A LEU* 4.0 13.9 - - - +
437A ILE* 3.5 5.0 - - - +
438A ARG 2.9 28.0 + - - +
448A TRP* 3.6 9.8 - - - -
449A THR* 1.3 78.9 - - - +
451A SER* 1.3 69.9 + - - +
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Residues in contact with SER 451 (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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105A GLY* 5.6 1.6 - - - -
106A ILE* 3.5 11.1 - - - +
117A ILE* 3.4 29.0 + - - +
118A ARG* 4.0 1.7 - - - -
120A PRO* 3.9 8.8 - - - +
167A PRO* 5.5 1.6 - - - +
435A GLU* 3.0 42.1 + - - +
436A MET 3.1 17.3 - - - -
437A ILE* 3.9 3.6 - - - -
450A SER* 1.3 83.1 + - - +
452A SER* 1.3 60.0 + - - +
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Residues in contact with SER 452 (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* 5.3 1.6 - - - -
103A ASP* 3.8 16.4 - - - -
104A ASN* 4.7 4.7 + - - -
105A GLY* 4.1 12.3 - - - -
106A ILE* 4.2 3.6 - - - -
117A ILE* 5.5 1.3 - - - -
120A PRO* 4.9 2.0 - - - -
435A GLU* 3.5 1.9 - - - -
436A MET* 2.7 43.9 + - - +
451A SER* 1.3 74.3 - - - +
453A SER* 1.3 60.8 + - - +
470A ASP* 2.6 39.8 + - - +
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Residues in contact with SER 453 (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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101A SER* 5.5 0.7 + - - -
102A LYS* 3.8 5.0 - - - +
103A ASP* 2.7 44.3 + - - +
120A PRO* 4.0 30.0 + - - +
122A VAL* 5.8 0.7 - - - +
131A THR* 4.9 9.2 + - - +
433A TRP* 5.4 3.4 - - - -
434A VAL 3.4 14.1 - - - -
436A MET* 3.8 7.5 - - - +
452A SER* 1.3 75.7 + - - +
454A ILE* 1.3 67.4 + - - +
455A VAL* 4.7 8.5 - - - +
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Residues in contact with ILE 454 (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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99A PRO* 5.0 4.3 - - + -
101A SER 3.3 17.5 - - - +
102A LYS* 4.6 5.8 - - + -
402A VAL* 4.2 6.1 - - + -
403A VAL* 4.8 5.4 - - + -
433A TRP* 3.4 1.4 - - - -
434A VAL* 3.0 40.7 + - + +
436A MET* 3.5 27.1 - - + -
453A SER* 1.3 75.2 - - - +
455A VAL* 1.3 72.1 + - - +
456A MET* 3.7 25.7 + - - +
468A TRP* 3.3 41.5 - - + +
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Residues in contact with VAL 455 (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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99A PRO* 3.6 3.3 - - - +
100A PHE* 2.6 49.1 + - + +
101A SER* 3.1 27.6 + - - +
122A VAL* 3.7 23.1 - - + -
131A THR* 5.4 0.9 - - - +
163A VAL* 3.9 5.6 - - + -
415A PHE* 3.6 29.8 - - + -
432A PHE 3.3 15.9 - - - +
433A TRP* 4.1 4.9 - - + -
453A SER* 4.7 7.4 - - - +
454A ILE* 1.3 79.8 - - - +
456A MET* 1.3 59.1 + - - +
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Residues in contact with MET 456 (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* 3.2 33.7 - - + +
98A ALA 3.2 15.5 - - - +
99A PRO* 3.5 17.7 - - + -
400A GLN* 3.8 12.1 - - - +
402A VAL* 4.0 18.4 - - + -
431A CYS* 3.2 4.7 - - - +
432A PHE* 2.8 74.6 + - + +
434A VAL* 5.6 0.2 - - + -
454A ILE* 3.7 31.0 - - + +
455A VAL* 1.3 74.2 - - - +
457A CYS* 1.3 62.9 + - - +
468A TRP* 4.2 7.9 - - + -
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Residues in contact with CYS 457 (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* 3.4 6.0 - - - -
98A ALA* 2.9 34.1 + - + +
100A PHE* 4.0 29.8 - - + +
415A PHE* 4.6 0.2 - - - -
417A LEU* 4.0 13.0 - - + -
429A VAL* 4.4 6.3 - - + -
430A PRO 3.7 0.7 - - - -
431A CYS* 2.0 44.9 - - - -
456A MET* 1.3 74.3 - - - +
458A GLY* 1.3 63.3 + - - +
459A VAL* 3.6 5.5 + - + +
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Residues in contact with GLY 458 (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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92A CYS* 5.9 1.0 - - - +
94A ALA* 4.0 14.1 - - - -
96A GLY 3.5 7.9 - - - -
97A PHE* 3.5 10.9 - - - -
425A LYS* 4.2 9.5 + - - -
429A VAL* 3.5 17.8 - - - +
430A PRO* 2.7 23.7 + - - +
457A CYS* 1.3 71.9 - - - +
459A VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 459 (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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94A ALA* 3.4 6.7 - - - +
95A LYS 3.2 21.7 + - - -
96A GLY 2.8 24.3 + - - +
97A PHE 4.1 0.7 - - - +
98A ALA* 3.7 25.1 - - + +
425A LYS* 4.9 4.5 - - - +
457A CYS* 3.7 4.5 - - + +
458A GLY* 1.3 79.3 - - - +
460A ASP* 1.3 63.7 + - - +
461A TYR* 3.3 27.8 + - + +
463A VAL* 4.1 14.8 - - + -
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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