Contacts of the strand formed by residues 2257 - 2263 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2046D SER* 4.7 1.2 - - - +
2050D ALA* 3.9 9.4 - - - +
2243D ARG* 3.4 34.4 + - + +
2244D VAL 3.3 14.4 - - - +
2245D LYS* 3.5 37.7 - - + +
2255D PHE 5.2 3.9 + - - +
2256D LYS* 1.3 77.0 - - - +
2258D ALA* 1.3 61.7 + - - +
2259D GLU* 4.3 5.6 - - + +
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Residues in contact with ALA2258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2046D SER* 3.4 26.9 - - - +
2047D LEU* 3.5 32.5 - - + +
2050D ALA* 4.2 2.4 - - + +
2242D THR 3.9 0.2 - - - +
2243D ARG* 3.3 3.3 - - - -
2244D VAL* 2.8 40.0 + - + +
2257D GLN* 1.3 75.3 - - - +
2259D GLU* 1.3 63.4 + - - +
2260D PHE* 4.3 7.1 - - + -
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Residues in contact with GLU2259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2235A GLU* 3.2 32.0 - - - +
2046D SER* 3.5 11.9 + - - -
2228D ILE* 4.0 13.8 - - + +
2241D GLU* 5.6 3.4 - - + +
2242D THR 3.2 6.3 - - - +
2243D ARG* 2.4 51.0 + - + -
2257D GLN* 4.3 5.5 - - + +
2258D ALA* 1.3 76.3 - - - +
2260D PHE* 1.3 64.2 + - - +
2273D GLU* 4.6 3.1 - - - +
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Residues in contact with PHE2260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2044D SER* 3.3 25.1 - - - -
2046D SER* 4.1 3.1 - - - -
2047D LEU* 4.8 2.2 - - + -
2075D LEU* 3.9 17.5 - - + -
2225D ILE* 4.6 0.2 - - + -
2241D GLU* 3.7 7.0 + - - +
2242D THR* 2.7 63.3 + - + +
2244D VAL* 3.7 26.0 - - + -
2258D ALA* 4.3 8.3 - - + -
2259D GLU* 1.3 77.7 - - - +
2261D GLN* 1.3 72.8 + - - +
2262D ILE* 3.8 17.0 - - + -
2268D ILE* 3.9 21.1 - - + -
2269D ASN 5.0 0.4 - - - +
2273D GLU* 3.6 26.0 - - + +
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Residues in contact with GLN2261 (chain D).
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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2234A GLY* 4.4 13.3 - - - +
2231D VAL* 3.6 25.9 - - + +
2240D SER 3.6 3.4 - - - -
2241D GLU* 3.2 34.9 + - - +
2260D PHE* 1.3 79.2 - - - +
2262D ILE* 1.3 59.7 + - - +
2263D LEU* 3.8 14.1 - - + +
2268D ILE* 3.4 3.8 - - - -
2269D ASN* 2.7 63.3 + - + +
2302D LYS* 5.3 13.3 - - - +
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Residues in contact with ILE2262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070D SER 4.3 2.0 - - - +
2071D GLY* 3.9 29.6 - - - +
2074D THR* 3.9 28.3 - - + +
2075D LEU* 5.4 1.3 - - + +
2103D TYR* 4.9 2.9 - - - +
2225D ILE* 4.8 1.3 - - + -
2239D GLY* 3.1 2.5 - - - -
2240D SER* 2.7 47.3 + - - +
2242D THR* 3.6 21.1 - - + +
2260D PHE* 3.8 21.1 - - + -
2261D GLN* 1.3 70.9 - - - +
2263D LEU* 1.3 68.7 + - - +
2264D TYR* 3.6 4.8 + - + -
2267D GLY* 3.5 8.7 - - - +
2268D ILE* 4.5 7.2 - - + -
2502D ADP 4.7 15.5 - - - +
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Residues in contact with LEU2263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2103D TYR* 4.7 0.2 + - - -
2231D VAL* 4.0 21.3 - - + -
2238D VAL* 3.8 16.8 - - + +
2239D GLY* 4.5 0.7 - - - -
2261D GLN* 3.8 17.9 - - + +
2262D ILE* 1.3 77.2 - - - +
2264D TYR* 1.3 64.1 + - - +
2265D GLY 3.4 0.2 + - - -
2266D GLU* 3.0 34.6 + - + +
2267D GLY* 2.8 41.9 + - - +
2269D ASN* 4.0 33.0 - - + +
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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