Contacts of the strand formed by residues 51 - 54 (chain F) in PDB entry 1C9T
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLN* 5.8 0.6 - - - +
46F LEU* 3.4 4.6 - - - +
47F ILE* 3.0 27.6 + - + -
48F ASN* 2.9 33.3 + - - +
50F GLN* 1.3 82.9 - - + +
52F VAL* 1.3 63.9 + - - +
87F LYS* 4.7 1.3 - - + -
89F ILE* 3.8 15.7 - - + -
105F LEU* 3.8 34.3 - - + -
106F ILE 3.2 21.5 - - - -
107F LYS* 3.6 45.7 - - + +
241F THR* 4.4 5.8 - - + -
242F ILE* 3.7 48.2 + - + +
245F ASN* 3.6 32.9 + - + -
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.8 25.8 - - + -
33F LEU* 4.8 2.5 - - + -
44F GLY* 4.2 3.4 - - - -
45F SER 3.2 14.6 - - - +
46F LEU* 4.1 14.4 - - + -
51F TRP* 1.3 80.1 - - - +
53F VAL* 1.3 66.8 + - - +
54F SER* 5.2 0.2 - - - -
65F VAL* 4.3 10.1 - - + -
105F LEU* 3.7 4.2 - - - -
106F ILE* 2.7 59.1 + - + +
108F LEU* 4.0 28.0 - - + -
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Residues in contact with VAL 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLY* 3.4 1.9 - - - -
45F SER* 2.9 44.2 + - - +
47F ILE* 3.4 22.5 - - + +
52F VAL* 1.3 70.8 - - - +
54F SER* 1.3 67.6 + - - +
103F ILE* 4.0 14.1 - - + -
104F MET 3.6 10.3 - - - +
105F LEU* 3.9 13.7 - - + -
196F GLY 4.1 1.2 - - - +
209F LEU* 3.3 33.9 - - + -
212F ILE* 4.0 20.4 - - + -
231F VAL* 5.6 0.7 - - + -
238F ILE* 4.6 4.5 - - + -
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Residues in contact with SER 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.9 11.4 - - - +
43F GLY 3.0 25.8 + - - -
44F GLY* 4.2 2.0 - - - -
52F VAL* 5.2 0.4 - - - -
53F VAL* 1.3 77.9 - - - +
55F ALA* 1.3 66.5 + - - +
58F CYS* 4.1 1.9 - - - +
103F ILE* 3.4 5.2 - - - -
104F MET* 2.7 54.6 + - - -
106F ILE* 4.6 5.8 - - - -
196F GLY* 3.2 12.5 - - - -
212F ILE* 3.6 13.5 - - - +
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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