Contacts of the strand formed by residues 2103 - 2106 (chain A) in PDB entry 6FF7
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 THR2103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2102A TYR* 1.3 77.8 - - - +
2104A TYR* 1.3 59.0 - - - +
2105A ILE 4.2 0.2 + - - -
2138A GLN 4.2 3.6 + - - -
2139A VAL* 3.5 12.4 - - - +
2140A LYS* 2.9 27.6 + - - +
2260A GLN* 3.7 25.8 - - - -
2261A MET* 5.1 0.9 - - - -
2262A LEU* 5.8 4.9 - - - -
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Residues in contact with TYR2104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2103A THR* 1.3 73.3 - - - +
2105A ILE* 1.3 61.3 + - - +
2106A LEU* 3.8 1.7 + - + +
2140A LYS* 3.4 11.4 - - + +
2142A ILE* 5.6 8.3 - - + +
2175A LEU* 6.1 4.5 - - + +
2260A GLN 3.8 9.3 + - - +
2261A MET* 3.7 6.9 - - + +
2262A LEU* 2.9 28.1 + - - +
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Residues in contact with ILE2105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2103A THR 4.2 0.2 + - - -
2104A TYR* 1.3 71.0 - - - +
2106A LEU* 1.3 60.4 + - - +
2107A PRO 4.4 0.2 - - - -
2139A VAL* 6.5 0.2 - - + -
2140A LYS 2.9 15.1 + - - +
2141A GLU* 3.5 11.8 - - + +
2142A ILE* 2.9 28.2 + - - +
2262A LEU* 3.3 14.6 - - + +
2264A SER* 5.1 13.9 - - - -
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Residues in contact with LEU2106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2104A TYR* 3.8 2.4 + - + +
2105A ILE* 1.3 74.7 - - - +
2107A PRO* 1.3 68.0 - - - +
2108A LYS 3.9 0.3 + - - -
2111A LEU* 6.2 1.3 - - + -
2142A ILE* 4.3 12.6 - - + +
2262A LEU 2.9 11.8 + - - +
2263A LEU* 3.4 24.1 - - + +
2264A SER 3.5 5.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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