Contacts of the strand formed by residues 1243 - 1248 (chain A) in PDB entry 4ABK
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 VAL1243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1241A ALA* 3.5 4.6 - - - +
1242A ASP* 1.3 77.5 - - - +
1244A ILE* 1.3 78.6 + - - +
1245A VAL* 4.1 12.6 - - + -
1297A ASN* 3.2 13.9 - - + +
1299A ILE* 3.8 30.3 - - + -
1314A VAL* 4.5 2.2 - - + -
1317A GLU 6.2 0.2 - - - -
1318A CYS* 3.7 20.9 - - - -
1321A LYS* 5.8 0.9 - - + -
1323A TYR* 3.6 32.5 - - + -
1325A SER 3.2 3.9 + - - +
1326A ILE* 3.4 3.4 - - + -
1327A CYS 2.9 25.5 + - - -
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Residues in contact with ILE1244 (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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1236A ILE* 4.0 29.4 - - + +
1237A THR* 6.3 0.2 - - - -
1239A GLU* 3.7 24.5 - - + +
1241A ALA* 4.5 4.7 - - + +
1243A VAL* 1.3 78.3 - - - +
1245A VAL* 1.3 71.5 + - - +
1262A ILE* 4.2 13.5 - - + -
1293A LEU* 4.3 23.1 - - + -
1294A ARG 4.3 2.0 - - - +
1295A CYS* 3.8 30.6 - - + +
1297A ASN 3.2 5.7 + - - -
1298A ILE* 3.2 11.5 - - + +
1299A ILE 3.1 21.1 + - - -
1327A CYS* 3.3 14.4 - - + -
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Residues in contact with VAL1245 (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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1236A ILE* 3.9 0.5 - - - +
1243A VAL* 4.1 7.2 - - + -
1244A ILE* 1.3 76.4 - - - +
1246A ASN* 1.3 71.8 + - - +
1262A ILE* 3.5 13.2 - - - +
1299A ILE 3.2 11.4 - - - +
1301A VAL* 3.9 21.3 - - + -
1314A VAL* 3.9 33.2 - - + -
1326A ILE* 4.2 3.1 - - + -
1327A CYS 2.9 15.1 - - - -
1328A LEU* 3.6 22.4 - - + -
1329A PRO* 3.1 27.0 - - + +
1331A ILE* 4.3 7.4 - - + -
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Residues in contact with ASN1246 (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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1244A ILE 4.0 1.4 + - - -
1245A VAL* 1.3 75.9 - - - +
1247A SER* 1.3 66.6 + - - +
1248A THR* 3.9 16.5 - - - -
1252A PHE 6.0 0.4 + - - -
1259A SER* 3.2 33.8 + - - +
1262A ILE* 3.6 25.6 - - + +
1263A LEU* 4.7 9.1 - - - +
1298A ILE* 3.9 7.6 - - + -
1299A ILE 2.9 6.1 + - - +
1300A HIS* 3.1 35.6 + - + +
1301A VAL* 2.9 31.8 + - - +
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Residues in contact with SER1247 (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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1245A VAL 4.3 0.6 + - - -
1246A ASN* 1.3 81.1 + - - +
1248A THR* 1.3 59.9 + - - +
1258A VAL* 3.9 20.9 - - - +
1259A SER* 3.7 10.4 + - - -
1301A VAL* 3.5 5.2 - - - -
1303A GLY* 3.3 13.7 - - - -
1329A PRO* 4.2 11.9 - - - +
1331A ILE* 3.5 20.3 - - - +
2389A AR6 2.6 38.8 + - - +
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Residues in contact with THR1248 (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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1246A ASN* 3.9 14.2 + - - +
1247A SER* 1.3 75.6 + - - +
1249A SER* 1.3 68.0 + - - +
1252A PHE* 3.5 39.4 - - + -
1254A LEU* 3.3 31.6 + - - +
1259A SER* 4.5 1.1 - - - -
1300A HIS* 4.0 13.2 - - + +
1301A VAL 2.8 19.4 + - - +
1302A ILE* 3.3 4.9 - - - +
1303A GLY 2.8 22.9 + - - -
2389A AR6 3.4 10.2 - - - +
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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