Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 4B92
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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A THR 3.7 8.7 + - - +
96A MET* 3.5 6.2 - - + -
97A ILE 3.5 9.9 + - - -
126A CYS* 1.3 93.0 - - - +
128A TYR* 1.3 60.5 + - - +
390A ARG* 4.2 2.6 + - - -
391A LYS* 2.7 33.7 + - - +
399A ASP* 4.5 0.5 - - - +
401A ASP* 4.7 1.6 - - - -
441A SER* 4.5 2.2 + - - -
442A ARG* 2.9 45.8 + - - +
460A LYS 3.2 16.0 + - - +
462A CYS* 3.5 20.4 - - - -
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Residues in contact with TYR 128 (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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82A PHE* 4.7 1.3 - + - -
96A MET* 3.9 5.6 - - - +
97A ILE* 3.1 33.0 - - + +
117A ARG* 3.1 16.3 + - - -
120A ALA* 3.7 21.8 - - + +
121A ASP* 2.3 38.5 + - - -
124A VAL* 3.8 33.2 - - + -
126A CYS 4.3 1.3 - - - +
127A ASP* 1.3 75.3 - - - +
129A ALA* 1.3 70.2 + - - +
130A LEU* 4.0 19.1 - - + -
460A LYS 3.2 6.6 + - - -
461A PHE* 3.3 39.0 - + - -
462A CYS* 2.9 31.0 + - - +
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Residues in contact with ALA 129 (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 MET* 4.0 6.3 - - + +
97A ILE 3.2 4.9 + - - +
98A ILE* 3.3 21.2 - - + -
99A GLY 2.6 30.7 + - - -
128A TYR* 1.3 79.7 - - - +
130A LEU* 1.3 64.4 + - - +
461A PHE* 4.2 9.2 - - + -
462A CYS 4.0 6.3 - - - +
464A LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 130 (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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82A PHE* 4.7 3.1 - - + -
98A ILE* 4.0 4.7 - - - -
99A GLY* 3.3 24.7 - - - +
101A VAL* 4.1 10.5 - - + -
113A TYR* 3.7 35.7 - - + +
116A CYS* 3.7 29.2 - - - -
117A ARG* 3.9 23.6 - - + +
128A TYR* 4.0 15.9 - - + -
129A ALA* 1.3 86.0 - - - +
131A HIS* 1.3 70.2 + - - +
132A VAL* 4.1 0.7 + - + -
153A GLY 5.1 1.5 + - - +
154A VAL* 4.2 20.5 - - - +
156A SER* 4.4 3.1 + - - +
461A PHE* 4.1 6.4 - - + -
464A LEU* 5.0 5.4 - - - +
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Residues in contact with HIS 131 (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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65A THR* 2.7 26.1 + - + -
98A ILE* 3.3 21.3 - - + +
99A GLY 2.7 21.1 + - - +
100A HIS* 3.5 38.4 - + + +
101A VAL* 2.9 32.1 + - - +
130A LEU* 1.3 74.7 - - - +
132A VAL* 1.3 62.0 + - - +
156A SER* 2.5 38.0 + - - +
158A GLN* 4.5 9.9 - - + -
189A ARG* 3.5 25.8 + - - -
385A LEU* 4.8 8.7 - - + -
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Residues in contact with VAL 132 (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 VAL* 3.8 14.4 - - + -
103A PRO* 4.6 1.1 - - + -
109A LEU* 3.9 40.2 - - + +
113A TYR* 4.2 17.0 - - + -
130A LEU 4.1 0.9 + - - +
131A HIS* 1.3 77.0 - - - +
133A GLY* 1.3 68.1 + - - +
148A LEU* 4.1 11.9 - - + -
154A VAL* 3.9 25.8 - - + -
156A SER 3.4 6.1 + - - -
157A PHE* 3.1 24.9 - - + -
158A GLN* 2.9 21.3 + - - -
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Residues in contact with GLY 133 (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 VAL 2.7 21.7 + - - -
102A LEU* 4.4 8.3 - - - -
103A PRO* 3.0 30.0 - - - +
109A LEU* 3.9 6.1 - - - +
131A HIS 4.1 0.2 - - - -
132A VAL* 1.3 72.9 - - - +
134A ILE* 1.3 61.7 + - - -
135A THR* 3.5 3.3 + - - -
158A GLN* 3.2 19.0 - - - +
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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