Contacts of the strand formed by residues 211 - 214 (chain A) in PDB entry 1BZH
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 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A SER 4.0 2.2 + - - +
81A TYR* 3.6 14.6 - - + -
82A ILE 2.9 25.8 + - - +
104A SER* 4.8 0.7 - - - -
105A ARG 5.7 0.2 - - - +
106A GLY* 3.5 23.1 - - - +
108A VAL* 3.6 28.3 - - + -
198A VAL* 4.7 4.7 - - + -
203A SER* 4.3 10.2 + - - +
204A LEU* 3.2 35.7 - - + +
209A GLY 3.5 3.0 + - - -
210A PRO* 1.3 71.2 - - - +
212A VAL* 1.3 63.6 + - - +
213A VAL* 3.5 17.9 - - + -
225A PHE* 4.9 0.9 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 3.6 24.5 - - + -
84A THR* 3.8 15.0 - - + -
95A PHE* 3.7 34.8 - - + -
98A MET* 4.1 8.5 - - + -
99A VAL* 4.3 13.2 - - + -
104A SER* 3.6 24.0 - - - +
106A GLY 3.1 12.8 + - - +
107A VAL* 3.2 9.4 - - + +
108A VAL 2.7 33.1 + - - +
211A VAL* 1.3 72.9 - - - +
213A VAL* 1.3 55.6 + - - +
214A HIS 5.2 0.2 - - - +
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Residues in contact with VAL 213 (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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81A TYR* 4.4 0.4 - - + -
82A ILE 2.7 9.3 + - - -
83A LEU* 3.3 15.3 - - + -
84A THR* 3.0 24.8 + - - +
108A VAL* 3.4 9.9 - - + +
110A LEU* 3.5 28.5 - - + -
211A VAL* 3.5 30.3 - - + +
212A VAL* 1.3 74.5 - - - +
214A HIS* 1.3 63.1 + - - +
222A SER* 3.5 21.0 + - - +
225A PHE* 3.9 25.1 - - + -
226A CYS* 4.0 8.3 - - - -
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Residues in contact with HIS 214 (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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84A THR* 2.9 33.2 - - + +
85A GLN 4.0 2.0 - - - +
86A GLY* 3.5 6.5 - - - -
87A PRO* 4.6 0.7 - - + -
95A PHE* 4.3 13.9 - + - -
107A VAL* 4.3 3.6 - - + -
108A VAL 2.8 18.5 + - - +
109A MET* 3.3 11.2 - - + +
110A LEU* 2.8 34.1 + - - +
111A ASN* 3.0 23.6 - - - -
121A CYS* 3.5 22.9 - - - -
124A TYR* 2.6 35.1 + + - -
213A VAL* 1.3 75.8 - - - +
215A CYS* 1.3 70.6 + - - +
222A SER* 3.3 8.5 - - - -
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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