Contacts of the strand formed by residues 1298 - 1307 (chain A) in PDB entry 3S2H
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 TYR1298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886A ILE* 4.0 7.0 - - + -
887A GLY* 5.0 7.0 - - - -
888A GLY 4.9 2.4 + - - +
944A ARG* 3.2 69.6 + - + +
947A PHE 4.0 1.7 + - - -
948A VAL 3.3 27.0 + - - -
949A ASP 3.6 13.9 - - - -
950A GLY* 3.6 20.2 - - - -
1290A LYS* 3.8 24.9 - - - +
1291A VAL* 3.7 13.7 - - - -
1292A PRO* 3.6 28.2 - - + +
1297A GLU* 1.3 76.9 - - - +
1299A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL1299 (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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1290A LYS* 4.2 4.9 - - - +
1291A VAL* 2.8 37.6 + - - +
1293A SER* 3.5 19.3 - - - -
1297A GLU* 3.3 35.9 - - - +
1298A TYR* 1.3 71.9 - - - +
1300A LYS* 1.4 72.5 + - - +
1301A GLU* 3.4 2.0 + - - +
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Residues in contact with LYS1300 (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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1288A ASP* 3.8 42.9 + - + +
1289A ARG 3.4 2.9 - - - +
1290A LYS* 3.8 29.9 - - + +
1299A VAL* 1.4 81.3 - - - +
1301A GLU* 1.3 57.4 + - - +
1302A PRO* 3.8 8.7 - - + +
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Residues in contact with GLU1301 (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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1125A ALA* 5.9 3.1 - - - +
1289A ARG* 2.8 44.2 + - + +
1291A VAL* 3.7 28.6 - - + +
1299A VAL 3.4 1.1 + - - +
1300A LYS* 1.3 69.3 - - - +
1302A PRO* 1.4 70.4 - - + +
1303A GLU* 3.4 2.8 + - + +
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Residues in contact with PRO1302 (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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1126A ALA* 4.1 14.9 - - - +
1286A LYS* 3.8 34.6 - - + -
1287A TYR 3.5 6.3 - - - +
1288A ASP* 3.3 27.8 - - - +
1300A LYS* 3.8 7.8 - - + +
1301A GLU* 1.4 87.2 - - + +
1303A GLU* 1.3 59.6 + - - +
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Residues in contact with GLU1303 (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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1119A TYR* 3.3 20.9 - - - +
1120A LEU* 5.9 2.9 - - - +
1125A ALA* 4.3 20.3 - - + +
1126A ALA* 5.0 2.9 - - + -
1286A LYS* 3.3 8.4 - - - +
1287A TYR* 2.6 52.6 + - + +
1289A ARG* 3.5 40.4 + - + -
1301A GLU* 3.4 3.8 + - + +
1302A PRO* 1.3 73.6 - - - +
1304A TRP* 1.4 65.8 + - - +
1305A VAL* 3.2 25.9 - - + +
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Residues in contact with TRP1304 (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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1120A LEU* 3.9 26.4 + - + +
1125A ALA 3.9 7.8 + - - +
1126A ALA* 3.5 30.7 + - - -
1127A ASP 4.0 7.4 - - - -
1128A GLN* 3.3 45.3 - - + +
1131A ALA* 4.0 21.5 - - + -
1284A MET* 3.9 26.7 - - + -
1285A MET* 3.3 28.3 - - - -
1286A LYS* 3.7 50.9 - - + +
1303A GLU* 1.4 78.8 - - - +
1305A VAL* 1.3 64.3 + - - +
1306A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL1305 (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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1117A THR* 4.5 10.3 - - + -
1118A VAL 3.4 20.9 - - - +
1119A TYR* 3.7 23.6 - - + -
1283A VAL 3.3 2.8 - - - +
1284A MET* 3.6 0.6 - - - -
1285A MET* 2.8 41.7 + - - +
1287A TYR* 3.8 39.7 - - + -
1303A GLU* 3.2 26.2 - - - +
1304A TRP* 1.3 77.0 - - - +
1306A LEU* 1.3 72.9 + - - +
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Residues in contact with LEU1306 (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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1116A LEU 3.4 4.3 - - - +
1117A THR* 3.5 2.9 - - - -
1118A VAL* 3.0 56.1 + - + +
1120A LEU* 5.0 11.0 - - + -
1131A ALA* 4.0 11.2 - - + +
1134A ILE* 3.8 24.5 - - + +
1135A ARG* 3.7 26.0 - - + +
1138A ILE* 4.4 1.8 - - + -
1282A VAL* 3.8 22.2 - - + -
1283A VAL 3.4 0.7 - - - -
1284A MET* 3.6 35.9 - - + +
1304A TRP* 6.5 0.2 - - + -
1305A VAL* 1.3 74.3 - - - +
1307A GLU* 1.3 58.1 + - - +
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Residues in contact with GLU1307 (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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1115A SER* 4.6 11.0 - - - -
1116A LEU 3.8 15.0 - - - -
1117A THR* 4.7 10.3 - - - -
1281A ARG 3.5 9.8 - - - +
1282A VAL* 3.3 13.0 - - - -
1283A VAL* 2.9 45.3 + - - +
1285A MET* 5.6 2.8 - - - +
1305A VAL* 3.9 1.0 + - - -
1306A LEU* 1.3 74.9 - - - +
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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