Contacts of the strand formed by residues 1224 - 1228 (chain M) in PDB entry 2JA7
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 LEU1224 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216M ILE* 4.7 5.6 - - + +
1217M LYS* 4.3 10.7 - - - +
1220M PHE* 3.3 53.8 - - + -
1221M LYS 4.0 9.9 + - - +
1223M ASP* 1.3 82.4 - - - +
1225M PHE* 1.3 61.5 + - - +
1226M VAL* 3.4 19.9 + - + +
1240M CYS* 3.9 21.8 - - + +
1241M ARG 2.9 35.9 - - - +
1242M VAL* 4.3 9.0 - - + +
1243M VAL* 4.6 2.2 - - - +
1260M LEU* 6.2 1.8 - - + -
1263M ILE* 4.8 12.3 - - + -
1267M MET* 5.8 1.3 - - + -
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Residues in contact with PHE1225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173M HIS* 4.4 24.7 - + - -
1188M GLN* 3.4 37.5 - - - +
1217M LYS* 4.2 17.0 - - - +
1224M LEU* 1.3 71.1 - - - +
1226M VAL* 1.3 66.0 + - - +
1227M ILE* 3.3 38.6 - - + -
1240M CYS* 3.1 7.9 - - - +
1241M ARG* 3.1 45.4 + - + +
1243M VAL* 4.5 10.0 - - + +
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Residues in contact with VAL1226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173M HIS* 5.9 1.7 - - - -
1213M GLY* 5.4 1.1 - - - -
1216M ILE* 4.8 11.7 - - + -
1217M LYS* 4.2 32.5 + - + +
1224M LEU* 3.4 27.1 + - + +
1225M PHE* 1.3 86.9 - - - +
1227M ILE* 1.3 75.0 + - - +
1228M TRP* 4.1 21.1 - - + -
1238M ILE* 3.6 23.6 - - + -
1239M ARG 3.3 12.3 - - - +
1240M CYS* 3.5 13.5 - - + -
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Residues in contact with ILE1227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169M ILE* 3.7 31.4 - - + +
1170M ILE* 5.2 14.1 - - + -
1173M HIS* 4.9 23.6 - - + +
1225M PHE* 3.3 35.9 - - + -
1226M VAL* 1.3 79.8 - - - +
1228M TRP* 1.3 87.3 + - - +
1238M ILE* 3.5 6.8 - - - +
1239M ARG* 2.9 48.5 + - + +
1241M ARG* 5.3 2.7 - - - +
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Residues in contact with TRP1228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169M ILE* 4.3 8.6 - - - +
1209M MET* 3.8 22.7 - - + +
1210M GLY* 4.0 26.5 - - - +
1213M GLY* 4.1 22.4 - - - -
1214M GLU* 4.0 25.6 - - + -
1217M LYS* 5.2 10.3 - - + -
1226M VAL* 4.1 22.2 - - + -
1227M ILE* 1.3 104.2 - - - +
1229M SER* 1.3 80.3 + - - +
1230M GLU* 5.1 2.7 - - + +
1237M ILE 3.3 14.4 - - - +
1238M ILE* 4.2 10.8 - - + -
1239M ARG* 4.9 0.7 - - - +
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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