Contacts of the strand formed by residues 125 - 129 (chain A) in PDB entry 2BZN
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 TYR 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.6 13.8 - + - -
43A GLN* 5.8 1.6 - - + +
44A THR 4.0 5.5 + - - -
45A TYR* 3.5 34.1 - + - +
73A PHE* 3.6 28.7 - + + -
97A GLU 3.5 21.1 - - - -
98A HIS* 4.9 1.3 - + - -
99A LEU 3.6 15.6 + - - +
100A ALA* 3.4 14.4 - - + -
101A ALA* 3.2 20.8 + - - +
117A LEU* 4.6 0.9 - - - +
123A VAL* 3.6 7.9 + - - +
124A LYS* 1.3 92.8 - - + +
126A ILE* 1.3 65.8 + - - +
153A THR* 3.3 40.6 - - + -
155A MET* 4.5 10.5 - - + -
175A ILE* 4.8 2.7 - - + -
238A PHE* 5.9 1.1 - + - -
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Residues in contact with ILE 126 (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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100A ALA* 4.4 2.0 - - - -
101A ALA 3.4 7.0 - - - +
113A LEU* 3.9 14.4 - - + -
117A LEU* 3.5 32.3 - - + -
125A TYR* 1.3 79.8 - - - +
127A CYS* 1.3 59.4 + - - +
128A LEU* 3.6 30.1 - - + -
145A VAL* 3.8 12.6 - - + -
149A PHE* 3.8 17.3 - - + -
152A HIS* 3.6 26.0 - - + -
153A THR 2.9 6.9 + - - +
154A ILE* 3.5 8.9 - - + -
155A MET* 2.7 35.5 + - - +
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Residues in contact with CYS 127 (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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54A ASN* 3.9 16.8 - - - -
75A ALA* 4.4 7.6 - - + -
100A ALA* 4.2 7.6 - - + +
101A ALA 2.9 9.6 + - - +
102A SER* 3.1 15.5 - - - +
103A SER 2.9 26.2 + - - +
126A ILE* 1.3 71.4 - - - +
128A LEU* 1.3 62.3 + - - +
129A ASP* 3.3 27.3 + - - +
155A MET* 3.6 21.1 - - - -
177A LYS* 4.0 20.0 - - - -
240A MET* 4.8 0.9 - - - -
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Residues in contact with LEU 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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103A SER* 3.4 14.8 - - - +
113A LEU* 4.6 1.6 - - + -
126A ILE* 3.6 24.2 - - + -
127A CYS* 1.3 75.0 - - - +
129A ASP* 1.3 59.2 + - - +
138A PHE* 3.7 15.7 - - + -
141A PHE* 3.7 26.0 - - + -
142A VAL* 4.1 20.4 - - + -
145A VAL* 3.8 30.5 - - + -
154A ILE* 3.8 19.7 - - + -
155A MET 2.8 14.9 + - - +
156A ALA* 3.3 4.0 - - - -
157A GLY 3.1 24.8 + - - +
177A LYS* 4.8 1.7 - - - +
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Residues in contact with ASP 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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54A ASN* 2.6 36.9 + - - +
78A LYS* 4.7 7.3 + - + +
102A SER* 5.8 0.2 - - - -
103A SER 3.1 11.7 + - - +
104A GLY* 3.6 15.4 - - - -
127A CYS* 3.3 11.3 - - - +
128A LEU* 1.3 74.0 - - - +
130A VAL* 1.3 75.5 + - - +
138A PHE* 4.4 1.8 - - - -
157A GLY 3.6 1.8 - - - -
158A ASN* 4.0 2.4 - - - +
177A LYS* 2.9 31.3 + - - -
1338A IMP 5.2 3.3 + - - -
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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