Contacts of the strand formed by residues 1301 - 1305 (chain C) in PDB entry 2XKK
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 LEU1301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256C ILE 3.0 4.2 - - - +
1257C VAL 3.5 0.2 - - - -
1258C ILE* 2.6 58.3 + - + +
1261C LEU* 5.3 5.8 - - + -
1267C GLY* 4.2 20.0 - - - +
1270C VAL* 3.4 35.2 - - + -
1271C ILE* 3.7 23.3 - - + +
1274C ILE* 5.3 2.7 - - + -
1289C VAL* 4.7 9.0 - - + -
1290C ARG 4.0 4.9 - - - +
1291C ASP* 4.0 24.0 - - - +
1299C THR* 4.5 12.5 - - + +
1300C ARG* 1.3 71.3 - - - +
1302C VAL* 1.3 61.8 + - - +
1303C ILE* 5.6 2.0 - - + -
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Residues in contact with VAL1302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255C GLU* 3.7 26.2 - - + -
1256C ILE 3.2 3.6 - - - +
1257C VAL* 3.5 26.9 - - + -
1288C ASP 4.3 0.2 - - - +
1289C VAL* 3.5 7.3 - - - +
1290C ARG* 2.9 39.8 + - + +
1292C GLU* 3.2 35.7 - - - +
1300C ARG 3.4 3.1 + - - +
1301C LEU* 1.3 74.4 - - - +
1303C ILE* 1.3 63.0 + - - +
1304C VAL* 3.9 14.5 + - + -
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Residues in contact with ILE1303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254C ASN 3.8 0.2 - - - +
1255C GLU* 2.9 7.4 - - - -
1256C ILE* 2.8 61.6 + - + +
1258C ILE* 4.4 13.7 - - + -
1274C ILE* 3.7 21.5 - - + -
1286C VAL* 3.7 32.3 - - + -
1288C ASP 4.1 1.3 - - - -
1289C VAL* 4.4 6.3 - - + -
1301C LEU* 5.0 3.6 - - + +
1302C VAL* 1.3 77.0 - - - +
1304C VAL* 1.3 63.5 + - - +
1305C LEU* 3.7 5.1 + - + -
1315C VAL* 5.2 0.4 - - + -
1316C MET* 4.2 7.0 - - - -
1319C LEU* 3.5 31.4 - - + -
1325C LEU* 5.2 1.6 - - + -
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Residues in contact with VAL1304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254C ASN* 4.0 12.3 - - - +
1255C GLU* 4.5 5.4 - - + +
1286C VAL* 3.2 5.1 - - - +
1287C VAL* 2.7 31.6 + - + -
1288C ASP* 2.8 43.0 + - + +
1289C VAL* 5.1 0.4 - - - -
1290C ARG* 5.2 3.4 - - + +
1302C VAL* 3.9 19.1 - - + +
1303C ILE* 1.3 76.1 - - - +
1305C LEU* 1.3 73.6 + - - +
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Residues in contact with LEU1305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251C ILE* 5.8 0.9 - - + -
1253C LYS 5.5 0.7 - - - +
1254C ASN* 2.9 42.0 + - + +
1256C ILE* 4.4 12.1 - - + -
1285C LEU 3.1 19.1 - - - +
1286C VAL* 4.0 8.1 - - + +
1287C VAL* 4.0 5.4 + - - +
1303C ILE* 4.4 4.9 - - + +
1304C VAL* 1.3 89.1 - - - +
1306C ARG* 1.3 65.8 + - - +
1307C SER 4.3 1.6 - - - +
1308C ASN 6.1 0.2 - - - +
1310C ILE* 4.2 17.3 - - + +
1312C ALA* 3.6 32.8 - - + +
1315C VAL* 3.7 37.5 - - + -
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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