Contacts of the strand formed by residues 2222 - 2227 (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 SER2222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2086A ARG* 4.0 13.0 - - - +
2089A HIS* 3.6 21.1 - - - -
2091A TYR* 6.0 4.0 - - - -
2218A PHE* 3.9 2.1 - - - +
2219A THR* 2.8 35.2 + - - +
2220A PRO 3.7 0.8 - - - -
2221A GLY* 1.3 80.1 - - - +
2223A CYS* 1.3 67.0 + - - +
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Residues in contact with CYS2223 (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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2086A ARG* 3.7 22.4 - - + +
2087A THR* 5.7 0.7 - - - -
2089A HIS 3.2 6.2 + - - +
2090A ILE* 4.8 4.5 - - + -
2091A TYR* 3.4 24.5 + - - +
2216A CYS 6.3 0.4 - - - -
2217A SER 3.4 11.9 - - - +
2218A PHE* 4.5 4.0 - - + +
2219A THR* 4.5 2.5 - - - +
2222A SER* 1.3 79.1 - - - +
2224A THR* 1.3 65.4 + - - +
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Residues in contact with THR2224 (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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2090A ILE* 5.9 0.2 - - - +
2091A TYR 3.4 20.0 - - - +
2093A SER* 4.9 11.0 - - - -
2216A CYS* 3.5 4.7 - - - +
2217A SER* 2.9 38.5 + - - -
2223A CYS* 1.3 77.1 - - - +
2225A LEU* 1.3 63.9 + - - +
2226A THR* 3.9 3.1 - - - -
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Residues in contact with LEU2225 (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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2091A TYR 4.6 2.2 + - - -
2092A VAL* 4.8 17.3 - - + +
2093A SER* 4.9 4.8 + - - -
2214A ILE* 6.1 3.6 - - + -
2215A THR 3.5 7.0 - - - -
2216A CYS* 4.7 4.0 - - + +
2224A THR* 1.3 74.3 - - - +
2226A THR* 1.3 62.4 + - - +
2227A ALA* 3.6 5.1 + - - +
2261A MET* 5.4 4.7 - - - +
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Residues in contact with THR2226 (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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2093A SER* 5.5 11.0 - - - -
2185A SER 4.8 13.0 - - - -
2213A ILE 4.1 0.7 - - - +
2214A ILE* 3.6 1.5 - - - -
2215A THR* 2.9 48.2 + - - -
2217A SER* 5.8 4.7 - - - -
2224A THR* 3.9 3.7 - - - -
2225A LEU* 1.3 71.5 - - - +
2227A ALA* 1.3 62.8 + - - +
2228A TYR* 4.1 0.5 + - - +
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Residues in contact with ALA2227 (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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2212A ILE* 6.0 2.0 - - + -
2213A ILE 3.8 4.7 - - - +
2214A ILE* 4.4 9.4 - - + +
2225A LEU 3.6 4.5 + - - +
2226A THR* 1.3 73.9 - - - +
2228A TYR* 1.3 64.6 + - - +
2258A ARG* 4.1 8.0 - - - +
2259A VAL* 4.1 30.6 + - + +
2260A GLN 5.2 0.9 - - - +
2261A MET* 4.4 20.2 - - + -
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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