Contacts of the strand formed by residues 2257 - 2263 (chain A) in PDB entry 3CMT
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 GLN2257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2046A SER* 4.8 1.2 - - - +
2050A ALA* 3.9 8.5 - - - +
2243A ARG* 3.3 35.0 + - + +
2244A VAL 3.2 13.0 - - - +
2245A LYS* 3.4 38.3 - - + +
2255A PHE 5.2 4.1 + - - +
2256A LYS* 1.3 77.3 - - - +
2258A ALA* 1.3 61.2 + - - +
2259A GLU* 4.3 4.2 - - + +
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Residues in contact with ALA2258 (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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2046A SER* 3.3 39.0 - - - +
2047A LEU* 3.5 22.0 - - + +
2050A ALA* 4.2 2.5 - - + -
2242A THR 3.9 0.2 - - - +
2243A ARG* 3.3 3.3 - - - +
2244A VAL* 2.8 40.1 + - + +
2257A GLN* 1.3 75.0 - - - +
2259A GLU* 1.3 62.3 + - - +
2260A PHE* 4.3 6.9 - - + -
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Residues in contact with GLU2259 (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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2046A SER* 3.5 12.0 + - - -
2228A ILE* 4.0 12.6 - - + +
2241A GLU* 5.6 3.8 - - + +
2242A THR 3.2 7.0 - - - +
2243A ARG* 2.4 49.2 + - + -
2257A GLN* 4.3 5.1 - - + +
2258A ALA* 1.3 74.8 - - - +
2260A PHE* 1.3 64.4 + - - +
2273A GLU* 4.5 3.5 - - - +
2235D GLU* 4.7 12.0 - - - +
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Residues in contact with PHE2260 (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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2044A SER* 3.3 24.2 - - - -
2046A SER* 4.1 2.9 - - - -
2047A LEU* 4.8 2.0 - - + -
2075A LEU* 3.9 18.2 - - + -
2225A ILE* 4.6 0.2 - - + -
2241A GLU* 3.7 7.3 + - - +
2242A THR* 2.7 61.7 + - + +
2244A VAL* 3.7 26.0 - - + -
2258A ALA* 4.3 9.4 - - + -
2259A GLU* 1.3 78.1 - - - +
2261A GLN* 1.3 73.3 + - - +
2262A ILE* 3.8 17.3 - - + -
2268A ILE* 3.8 20.6 - - + -
2269A ASN 5.0 0.4 - - - +
2273A GLU* 3.5 27.4 - - + +
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Residues in contact with GLN2261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2231A VAL* 3.5 25.7 - - + +
2240A SER 3.6 3.6 - - - -
2241A GLU* 3.2 34.5 + - - +
2260A PHE* 1.3 77.2 - - - +
2262A ILE* 1.3 61.4 + - - +
2263A LEU* 3.8 13.7 - - + +
2268A ILE* 3.4 4.2 - - - -
2269A ASN* 2.8 63.2 + - + +
2302A LYS* 5.3 10.4 - - - +
2234D GLY* 4.6 15.6 - - - +
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Residues in contact with ILE2262 (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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2070A SER 4.3 2.0 - - - +
2071A GLY* 4.0 29.8 - - - +
2074A THR* 3.8 28.0 - - + +
2075A LEU* 5.4 1.3 - - + +
2103A TYR* 4.9 2.5 - - - +
2225A ILE* 4.8 2.0 - - + -
2239A GLY* 3.1 2.8 - - - -
2240A SER* 2.7 46.6 + - - +
2242A THR* 3.7 20.2 - - + +
2260A PHE* 3.8 19.1 - - + -
2261A GLN* 1.3 75.6 - - - +
2263A LEU* 1.3 65.7 + - - +
2264A TYR* 3.6 4.7 + - + -
2267A GLY* 3.5 8.7 - - - +
2268A ILE* 4.4 7.2 - - + -
2502A ADP 4.6 16.2 - - - +
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Residues in contact with LEU2263 (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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2103A TYR* 4.7 0.7 + - - -
2231A VAL* 4.0 27.8 - - + -
2238A VAL* 3.8 17.9 - - + +
2239A GLY* 4.5 0.9 - - - -
2261A GLN* 4.0 12.1 - - + +
2262A ILE* 1.3 76.2 - - - +
2264A TYR* 1.3 63.6 + - - +
2265A GLY 3.3 0.2 + - - -
2266A GLU* 3.0 35.5 + - + +
2267A GLY* 2.8 41.7 + - - +
2269A ASN* 4.0 33.7 - - + +
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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