Contacts of the strand formed by residues 1147 - 1153 (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 THR1147 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143M LEU* 2.7 40.8 + - - +
1144M LYS* 4.0 4.1 + - - +
1145M SER 3.7 0.9 - - - -
1146M VAL* 1.3 78.7 - - - +
1148M ILE* 1.3 65.4 + - - +
1149M ALA 3.6 19.3 - - - +
1150M SER* 5.2 0.4 - - - -
1195M LEU* 4.5 13.3 - - + +
1196M GLU 4.0 4.3 - - - +
1197M LEU* 3.6 9.5 - - + +
1268M LEU* 4.2 10.2 - - + +
48U LEU* 3.4 39.2 - - + +
49U ILE* 4.4 7.7 - - - +
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Residues in contact with ILE1148 (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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1147M THR* 1.3 74.9 - - - +
1149M ALA* 1.3 58.5 + - + +
1196M GLU* 2.5 42.3 + - + +
1197M LEU 3.7 6.5 - - - +
1198M ASP* 3.5 51.1 - - + +
45U ARG* 5.5 2.0 - - - +
47U GLU* 3.5 3.9 - - + +
48U LEU* 2.6 29.0 + - - -
49U ILE* 3.2 31.6 + - + +
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Residues in contact with ALA1149 (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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1147M THR* 3.6 8.1 - - - +
1148M ILE* 1.3 87.0 - - + +
1150M SER* 1.3 61.6 + - - +
1151M GLU* 5.1 5.0 - - + +
1194M ARG 3.8 0.7 - - - +
1195M LEU* 3.4 2.3 - - - -
1196M GLU* 2.9 33.2 + - + +
45U ARG* 4.0 25.8 - - + +
47U GLU* 3.3 25.6 - - + +
48U LEU* 4.0 2.9 - - - +
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Residues in contact with SER1150 (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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1147M THR* 4.7 2.7 - - - +
1149M ALA* 1.3 73.9 - - - +
1151M GLU* 1.3 65.9 + - - +
1152M ILE* 6.4 0.2 - - - -
1193M LEU* 4.6 3.6 - - - -
1194M ARG 3.2 5.4 - - - -
1195M LEU* 3.1 23.8 - - - -
1264M GLU* 2.8 37.8 + - - -
1268M LEU* 5.3 3.1 - - - -
44U TYR* 4.5 3.6 - - - -
45U ARG* 3.3 0.5 - - - -
46U HIS* 2.8 43.6 + - - +
48U LEU* 5.5 0.4 - - - +
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Residues in contact with GLU1151 (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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1149M ALA* 5.3 4.8 - - - +
1150M SER* 1.3 81.1 - - - +
1152M ILE* 1.3 64.2 + - - +
1153M TYR* 3.3 31.1 + - + -
1193M LEU* 3.1 6.1 - - - +
1194M ARG* 2.7 72.0 + - + +
1196M GLU* 5.4 5.9 + - - +
42U LEU* 4.2 7.2 - - + +
44U TYR 2.9 10.5 - - - +
45U ARG* 3.2 50.3 + - + +
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Residues in contact with ILE1152 (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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1151M GLU* 1.3 76.8 - - - +
1153M TYR* 1.3 63.9 + - - +
1191M TRP* 5.1 6.3 - - + -
1192M LEU 3.0 17.0 - - - +
1193M LEU* 4.5 7.9 - - + -
1257M ASP* 5.1 9.2 - - + +
1260M LEU* 3.9 39.3 - - + +
1261M LYS* 4.1 17.3 - - + +
1264M GLU* 5.4 2.9 - - + -
43U VAL* 3.1 32.5 + - + +
44U TYR* 2.8 52.1 + - + -
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Residues in contact with TYR1153 (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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1151M GLU* 3.3 48.7 + - + -
1152M ILE* 1.3 76.7 - - - +
1154M TYR* 1.3 62.7 + - - +
1155M ASP* 3.8 2.5 - - + +
1162M VAL* 6.2 0.2 - - + -
1163M ILE* 3.3 42.3 - - + +
1191M TRP* 3.1 12.9 - - - -
1192M LEU* 3.0 41.3 + - + -
1194M ARG* 3.6 21.2 + - + -
41U PRO* 3.2 21.1 - - + +
42U LEU* 3.3 32.5 - - + +
43U VAL 4.4 0.2 - - - +
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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