Contacts of the strand formed by residues 1319 - 1327 (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 ASN1319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1284C LEU 3.6 0.9 - - - +
1285C PHE* 3.4 4.0 - - - -
1286C VAL* 2.8 43.2 + - + +
1287C ASN 6.3 0.4 - - - -
1288C GLN* 5.9 2.8 - - - +
1312C SER* 6.1 1.4 - - - -
1313C ALA 3.9 7.4 - - - +
1314C MSE 5.0 14.2 - - - +
1317C ASP 3.7 6.1 + - - -
1318C TYR* 1.3 76.1 - - - +
1320C PHE* 1.3 59.3 + - - +
1321C VAL* 5.9 0.4 - - - -
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Residues in contact with PHE1320 (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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1149C MSE 3.4 39.9 - - + -
1157C TRP* 3.1 27.6 - + - -
1283C THR* 3.7 25.4 - - - -
1284C LEU 3.2 25.8 - - - -
1285C PHE* 3.7 28.9 - + + -
1312C SER* 3.2 6.8 - - - -
1313C ALA* 2.9 33.4 + - + +
1315C PHE* 3.4 32.1 - + + -
1319C ASN* 1.3 77.7 - - - +
1321C VAL* 1.3 71.4 - - - +
1322C PHE* 3.7 11.2 - - + -
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Residues in contact with VAL1321 (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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1282C THR* 3.8 1.4 + - - +
1283C THR* 3.4 2.8 - - - -
1284C LEU* 2.8 67.5 + - + +
1286C VAL* 6.0 0.7 - - + -
1299C PRO* 5.9 7.2 - - + -
1300C GLN* 6.0 1.8 - - - +
1310C CYS* 4.5 10.8 - - - -
1311C GLN 3.6 9.6 - - - +
1312C SER* 4.7 5.8 - - - -
1319C ASN 5.9 0.2 - - - -
1320C PHE* 1.3 81.4 - - - +
1322C PHE* 1.3 64.0 + - - +
1323C THR* 4.1 21.3 - - + -
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Residues in contact with PHE1322 (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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1149C MSE 3.4 30.5 - - + -
1150C GLY* 3.5 30.5 - - - -
1155C ASP 4.1 8.5 - - - -
1156C CYS* 4.5 1.1 - - - -
1157C TRP* 3.9 28.9 - - + -
1281C VAL* 3.9 26.0 - - + -
1282C THR 3.2 14.4 - - - -
1283C THR* 4.2 7.0 - - + -
1309C ASP* 4.4 7.2 - - + -
1310C CYS* 3.3 2.6 - - - -
1311C GLN* 2.8 41.0 + - + +
1320C PHE* 3.7 6.1 - - + -
1321C VAL* 1.3 73.3 - - - +
1323C THR* 1.3 65.0 + - - +
1324C SER* 4.0 28.0 - - - -
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Residues in contact with THR1323 (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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1281C VAL* 3.2 5.4 - - - +
1282C THR* 2.4 59.3 + - - +
1299C PRO* 4.6 17.9 - - + +
1300C GLN* 5.3 1.1 - - - +
1307C ARG* 4.7 4.3 - - - -
1309C ASP 3.3 9.2 - - - -
1310C CYS* 4.1 20.9 - - + -
1321C VAL* 4.1 11.9 - - + -
1322C PHE* 1.3 82.8 - - - +
1324C SER* 1.3 61.3 + - - +
1325C PHE* 3.0 28.6 - - + -
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Residues in contact with SER1324 (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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1155C ASP* 4.3 13.0 + - - +
1280C PHE 3.7 3.4 + - - -
1281C VAL* 3.4 16.4 - - - +
1307C ARG* 3.4 6.4 - - - +
1308C LEU* 2.8 42.8 + - - +
1309C ASP* 3.0 33.7 + - - -
1322C PHE* 4.0 12.1 - - - -
1323C THR* 1.3 74.9 - - - +
1325C PHE* 1.3 57.6 + - - +
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Residues in contact with PHE1325 (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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1268C ILE* 6.2 0.7 - - + -
1279C LYS* 3.3 4.8 - - - +
1280C PHE* 2.6 81.0 + + + +
1282C THR* 4.8 1.6 - - + -
1299C PRO* 4.5 4.9 - - + -
1300C GLN 4.4 14.1 - - - -
1301C LYS* 4.6 3.1 - - - -
1302C ILE* 3.6 31.4 - - + -
1305C PHE* 4.0 18.2 - - + -
1306C LYS 3.5 2.0 - - - -
1307C ARG* 3.5 42.8 - - + -
1308C LEU* 4.5 3.2 - - - +
1323C THR* 3.0 31.9 - - + -
1324C SER* 1.3 76.2 + - - +
1326C ALA* 1.3 59.9 + - - +
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Residues in contact with ALA1326 (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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1278C GLY 3.8 6.1 - - - +
1279C LYS* 4.0 9.9 - - + +
1305C PHE* 3.7 4.0 - - - -
1306C LYS* 2.7 38.5 + - + +
1308C LEU* 3.6 30.7 - - + -
1325C PHE* 1.3 75.5 - - - +
1327C LYS* 1.3 63.5 + - - +
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Residues in contact with LYS1327 (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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1276C LYS* 4.9 9.5 + - - +
1277C PRO 3.2 24.5 + - - -
1278C GLY* 2.8 24.3 + - - +
1304C GLY* 3.4 18.8 - - - +
1305C PHE* 3.4 25.9 - - + -
1306C LYS* 5.5 0.3 - - - +
1326C ALA* 1.3 76.0 - - - +
1328C LYS* 1.3 62.1 + - - +
1329C GLN* 2.5 64.4 + - + +
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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