Contacts of the strand formed by residues 96 - 102 (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 GLY 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ALA* 3.2 4.2 + - - +
95A LYS* 1.3 80.1 - - - +
97A PHE* 1.3 70.5 + - - -
366A TRP* 4.4 1.8 - - - -
400A GLN* 3.8 9.2 - - - -
458A GLY* 3.5 4.9 - - - -
459A VAL* 2.8 31.4 + - - +
461A TYR 3.2 15.3 + - - -
463A VAL 4.6 2.9 - - - -
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Residues in contact with PHE 97 (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* 5.1 2.2 - - + -
96A GLY* 1.3 81.0 - - - -
98A ALA* 1.3 59.7 + - - +
359A PHE* 4.8 4.5 - + - -
366A TRP* 3.7 34.1 - + + -
381A ILE* 3.4 40.6 - - + -
400A GLN* 2.8 37.6 + - - +
430A PRO* 3.8 23.8 - - + -
431A CYS 4.8 0.2 - - - -
432A PHE* 3.5 26.9 - + + -
456A MET* 3.2 17.9 - - + +
457A CYS* 3.4 7.9 - - - +
458A GLY* 3.5 31.6 - - - -
463A VAL* 3.3 13.6 - - - +
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Residues in contact with ALA 98 (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* 1.3 73.4 - - - +
99A PRO* 1.3 75.0 - - + +
456A MET* 3.2 5.5 - - - -
457A CYS* 2.9 32.9 + - + +
459A VAL* 3.7 27.1 - - + +
463A VAL* 4.4 7.0 - - + -
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Residues in contact with PRO 99 (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 4.3 0.7 - - - +
98A ALA* 1.3 89.1 - - + +
100A PHE* 1.3 62.8 + - - +
101A SER 5.1 1.8 - - - +
454A ILE* 5.0 4.7 - - + -
455A VAL 3.8 0.7 - - - +
456A MET* 3.7 25.4 - - + -
463A VAL* 4.8 6.1 - - + -
468A TRP* 3.9 36.3 - - + +
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Residues in contact with PHE 100 (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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98A ALA 3.3 2.2 + - - -
99A PRO* 1.3 74.7 - - - +
101A SER* 1.3 63.2 + - - +
129A CYS* 4.1 24.0 - - + -
163A VAL* 3.7 31.6 - - + -
415A PHE* 4.7 2.9 - + - -
417A LEU* 4.7 9.4 - - + -
455A VAL* 2.6 41.9 + - + +
456A MET* 4.6 0.4 - - - -
457A CYS* 4.0 22.4 - - + +
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Residues in contact with SER 101 (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* 3.9 1.9 - - - +
100A PHE* 1.3 87.3 - - - +
102A LYS* 1.3 67.3 + - - +
103A ASP* 5.0 0.3 + - - +
163A VAL* 3.5 12.0 - - - +
164A GLY* 3.5 28.0 + - - -
453A SER* 5.5 0.7 + - - -
454A ILE* 3.3 9.9 - - - +
455A VAL* 3.1 42.0 + - - +
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Residues in contact with LYS 102 (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* 1.3 79.1 - - - +
103A ASP* 1.3 63.4 + - - +
104A ASN* 2.4 46.4 + - - +
107A ARG* 5.1 0.6 - - - +
164A GLY* 3.6 8.2 - - - +
436A MET* 4.3 7.2 - - - -
452A SER* 5.3 1.3 - - - +
453A SER 3.8 11.4 - - - +
454A ILE* 4.6 4.5 - - + -
468A TRP* 3.2 37.7 - - + +
469A HIS 3.1 29.4 + - - -
470A ASP* 3.7 7.0 + - - +
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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