Contacts of the strand formed by residues 1207 - 1211 (chain E) in PDB entry 5B2G
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 GLN1207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1198E PHE* 2.9 46.1 + - + +
1199E ILE* 4.8 2.2 - - - -
1203E ILE* 5.3 0.9 - - + -
1205E THR* 4.3 6.6 + - - +
1206E SER* 1.3 76.0 - - - +
1208E THR* 1.3 64.4 + - - +
1209E ILE* 3.2 11.2 - - + +
1218E VAL* 3.7 26.5 - - + +
1219E VAL 3.4 7.9 - - - +
1220E GLN* 3.9 19.1 + - + +
218F ASN* 3.2 17.0 + - - +
220F ALA* 4.3 9.1 - - - +
222F ASN* 4.7 7.9 - - - +
223F LEU* 3.1 36.0 - - + +
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Residues in contact with THR1208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195E VAL* 4.7 10.3 - - + -
1196E THR 3.7 10.8 - - - +
1197E ALA* 4.1 14.9 - - + +
1199E ILE* 3.7 22.0 - - - +
1207E GLN* 1.3 76.7 + - - +
1209E ILE* 1.3 62.3 + - - +
1210E TRP* 3.8 24.7 + - + +
1219E VAL* 2.9 38.0 + - - +
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Residues in contact with ILE1209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194E ARG 4.2 0.2 - - - +
1195E VAL* 3.9 3.5 - - - +
1196E THR* 2.9 44.2 + - - +
1198E PHE* 4.2 8.5 - - + -
1207E GLN* 3.2 20.4 - - + +
1208E THR* 1.3 71.4 - - - +
1210E TRP* 1.3 64.9 + - - +
1211E GLU* 3.7 27.0 + - + +
1216E ASN* 4.7 12.6 - - + +
1217E CYS 4.0 6.7 - - - +
1218E VAL* 3.8 16.8 - - + +
218F ASN* 3.2 26.2 - - - +
223F LEU* 3.6 16.8 - - + +
224F TYR* 6.1 0.2 - - - -
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Residues in contact with TRP1210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191E PRO* 3.3 15.4 - - + +
1192E MET* 3.2 43.5 - - + -
1194E ARG 4.2 2.2 - - - -
1195E VAL* 3.7 37.2 - - + +
1208E THR* 3.8 22.8 + - + +
1209E ILE* 1.3 70.8 - - - +
1211E GLU* 1.3 60.2 + - - +
1216E ASN* 3.4 4.2 - - - +
1217E CYS* 3.0 46.9 + - + +
1219E VAL* 4.6 15.5 - - + +
1225E MET* 5.7 3.1 - - - -
1324E GLY* 5.3 0.2 - - - -
1325E ALA* 4.1 13.2 - - + -
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Residues in contact with GLU1211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191E PRO 3.3 4.0 - - - -
1192E MET* 4.9 0.2 - - - +
1193E TRP* 2.8 28.2 + - - +
1194E ARG* 3.1 59.8 + - + +
1196E THR* 3.9 17.9 + - - +
1209E ILE* 3.7 22.4 + - + -
1210E TRP* 1.3 69.2 - - - +
1212E GLY* 1.3 52.5 + - - +
1216E ASN* 4.0 15.5 + - + +
1230E TYR* 4.3 11.6 + - - +
1321E ARG* 4.2 8.7 + - - -
224F TYR* 5.4 7.6 - - - -
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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