Contacts of the strand formed by residues 51 - 54 (chain A) in PDB entry 2ZDL
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 TRP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.5 4.1 - - - +
47A ILE* 2.9 43.6 + - + +
48A ASN* 3.1 29.0 + - - +
50A GLN* 1.3 94.2 - - + +
52A VAL* 1.3 64.1 + - - +
87A LYS* 4.3 4.0 - - + -
89A ILE* 4.2 13.0 - - + -
105A LEU* 3.9 33.9 - - + -
106A ILE 3.4 18.8 - - - -
107A LYS* 3.5 46.7 - - + +
108A LEU* 4.5 0.4 - - - +
241A THR 4.8 0.2 - - - -
242A ILE* 3.4 40.5 + - + +
245A ASN* 3.6 35.8 + - + -
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Residues in contact with VAL 52 (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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31A VAL* 3.9 22.4 - - + -
33A LEU* 4.7 2.2 - - + -
44A GLY* 4.1 2.5 - - - -
45A SER 3.3 10.3 - - - +
46A LEU* 3.9 19.3 - - + -
47A ILE* 4.8 0.4 - - - -
51A TRP* 1.3 79.1 - - - +
53A VAL* 1.3 76.2 + - - +
54A SER 4.2 0.4 + - - +
65A VAL* 3.9 24.7 - - + -
104A MET 4.0 0.2 - - - +
105A LEU* 3.4 8.2 - - - +
106A ILE* 2.8 55.0 + - + +
108A LEU* 4.1 10.1 - - + -
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Residues in contact with VAL 53 (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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44A GLY* 3.4 3.3 - - - -
45A SER* 2.8 36.5 + - - +
47A ILE* 3.9 19.3 - - + -
52A VAL* 1.3 72.4 - - - +
54A SER* 1.3 64.5 + - - +
103A ILE* 4.0 11.4 - - + -
104A MET 3.6 2.0 - - - -
105A LEU* 3.5 25.8 - - + -
123A LEU* 5.1 0.2 - - + -
196A GLY 3.8 2.1 - - - +
209A LEU* 4.3 17.3 - - + -
212A ILE* 3.4 31.6 - - + -
231A VAL* 5.3 0.7 - - + -
238A ILE* 4.2 17.0 - - + -
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Residues in contact with SER 54 (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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33A LEU* 3.7 19.0 - - - +
43A GLY 2.8 26.1 + - - -
44A GLY* 4.3 1.8 - - - -
52A VAL* 4.1 0.8 + - - -
53A VAL* 1.3 73.7 - - - +
55A ALA* 1.3 68.7 + - - +
58A CYS* 3.8 5.4 - - - -
103A ILE* 3.4 5.0 - - - -
104A MET* 2.8 35.4 + - - +
106A ILE* 4.3 8.1 - - - -
196A GLY* 3.4 11.1 - - - -
212A ILE* 3.6 14.1 - - - +
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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