Contacts of the strand formed by residues 1279 - 1286 (chain C) in PDB entry 1I7M
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 LYS1279 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155C ASP* 3.2 37.7 + - - +
1182C SER* 3.1 49.3 + - - +
1183C GLU* 3.5 36.6 + - - +
1277C PRO* 3.3 4.6 - - - +
1278C GLY* 1.3 81.3 - - - +
1280C PHE* 1.3 70.4 + - - +
1305C PHE* 4.5 0.4 - - - -
1308C LEU* 6.3 0.2 - - + -
1325C PHE 3.3 13.9 - - - +
1326C ALA* 4.0 11.2 - - + +
1327C LYS 4.4 0.2 - - - +
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Residues in contact with PHE1280 (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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1115C LYS* 6.3 0.2 - - - +
1179C ILE* 3.8 11.2 - - + -
1180C LEU 3.1 16.6 - - - +
1181C MSE 3.8 12.3 - - + -
1182C SER* 5.8 0.2 - - - -
1268C ILE* 4.4 4.5 - - + -
1272C VAL* 3.9 24.9 - - + -
1277C PRO* 3.9 17.0 - - + -
1279C LYS* 1.3 76.9 - - - +
1281C VAL* 1.2 66.7 + - - +
1282C THR* 3.4 30.3 - - + -
1302C ILE* 4.1 13.0 - - + -
1305C PHE* 4.1 22.2 - + - -
1324C SER* 4.2 0.3 + - - -
1325C PHE* 2.6 77.3 + + + +
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Residues in contact with VAL1281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115C LYS* 3.9 19.1 - - + -
1155C ASP* 4.2 19.1 - - + -
1157C TRP* 6.2 0.9 - - + -
1179C ILE* 3.5 3.6 - - - -
1180C LEU* 2.7 63.1 + - + +
1280C PHE* 1.2 77.7 - - - +
1282C THR* 1.4 62.6 - - - +
1283C THR* 6.0 0.9 - - + -
1322C PHE* 3.9 20.0 - - + -
1323C THR 3.2 8.1 - - - +
1324C SER* 3.4 27.1 - - - +
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Residues in contact with THR1282 (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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1177C LEU* 4.7 3.1 - - - -
1178C GLU 3.3 12.3 - - - +
1179C ILE* 4.3 7.4 - - + -
1180C LEU* 5.8 0.2 - - - -
1268C ILE* 4.2 25.3 - - + +
1280C PHE* 3.4 31.2 - - + -
1281C VAL* 1.4 74.3 - - - +
1283C THR* 1.3 65.6 + - - +
1284C LEU* 6.0 0.4 - - - +
1299C PRO* 5.4 3.1 - - - +
1321C VAL 3.8 0.9 + - - +
1322C PHE* 3.2 8.9 - - - -
1323C THR* 2.4 59.8 + - - +
1325C PHE* 4.8 1.1 - - + -
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Residues in contact with THR1283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157C TRP* 3.6 43.7 - - + +
1176C THR 4.3 1.4 + - - -
1177C LEU* 3.3 6.8 - - - +
1178C GLU* 3.1 55.7 + - + +
1180C LEU* 5.1 5.6 - - + -
1281C VAL* 5.8 0.9 - - + -
1282C THR* 1.3 79.5 - - - +
1284C LEU* 1.3 62.9 + - - +
1285C PHE* 5.1 4.0 - - - -
1320C PHE* 3.7 16.6 - - + -
1321C VAL 3.4 5.8 - - - -
1322C PHE* 4.2 6.5 - - + -
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Residues in contact with LEU1284 (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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1176C THR 3.2 20.9 - - - +
1177C LEU* 3.9 13.2 - - + -
1264C TYR* 3.6 44.4 - - + -
1282C THR* 6.0 0.4 - - - +
1283C THR* 1.3 76.8 - - - +
1285C PHE* 1.3 69.4 + - - +
1286C VAL* 3.7 17.2 - - + +
1292C CYS 5.3 1.1 - - - +
1299C PRO* 5.4 9.9 - - + -
1319C ASN 3.6 0.9 - - - +
1320C PHE* 3.2 11.2 - - - -
1321C VAL* 2.8 58.6 + - + +
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Residues in contact with PHE1285 (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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1111C PHE* 3.5 33.7 - + - -
1157C TRP* 3.8 26.2 - + - -
1159C LEU* 4.1 4.7 - - + -
1175C GLN* 3.0 8.4 - - - +
1176C THR* 2.8 38.2 + - + +
1178C GLU* 5.5 0.9 - - - -
1283C THR* 5.1 4.9 - - - -
1284C LEU* 1.3 76.1 - - - +
1286C VAL* 1.3 61.6 + - - +
1287C ASN 4.3 0.2 - - - -
1315C PHE* 4.1 14.1 - + - -
1318C TYR* 3.9 21.3 - - + -
1319C ASN 3.4 4.7 - - - -
1320C PHE* 3.7 27.8 - + + -
1350D PUT 3.6 49.6 - - + -
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Residues in contact with VAL1286 (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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1174C ASP 3.8 4.0 - - - -
1175C GLN* 4.2 4.7 - - + -
1284C LEU* 3.7 27.8 - - + +
1285C PHE* 1.3 79.9 - - - +
1287C ASN* 1.3 68.7 + - - +
1290C SER* 3.6 29.4 - - - +
1292C CYS* 3.9 27.6 - - + +
1318C TYR* 4.0 1.1 - - - -
1319C ASN* 2.8 42.7 + - + +
1321C VAL* 6.0 0.4 - - + -
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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