Contacts of the strand formed by residues 1405 - 1414 (chain C) in PDB entry 3B13
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 TYR1405 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348C TYR* 2.9 59.3 + - + +
1349C GLY* 4.4 2.0 - - - -
1352C PHE* 3.6 0.6 - - - -
1386C GLU* 3.0 40.4 - - + -
1388C MET* 3.9 22.4 - - + -
1398C VAL* 4.1 17.5 - - + -
1401C ALA* 3.9 23.9 - - + +
1402C PRO* 5.4 0.7 - - - +
1403C GLY* 3.7 30.5 + - - -
1404C GLN* 1.3 73.9 - - - +
1406C ILE* 1.3 62.4 + - - +
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Residues in contact with ILE1406 (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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1345C VAL* 3.9 17.7 - - + -
1346C GLY 3.3 9.2 - - - +
1347C TYR* 3.9 14.4 - - + -
1352C PHE* 3.7 18.8 - - + -
1375C GLN* 4.7 4.7 + - - +
1378C LEU* 4.2 8.7 - - + -
1379C MET* 3.7 24.5 - - - -
1382C PHE* 3.9 23.3 - - + -
1385C ALA* 3.6 25.1 - - + -
1386C GLU 2.8 13.9 + - - +
1387C LYS* 3.6 4.2 - - - +
1388C MET* 2.8 27.6 + - - +
1405C TYR* 1.3 71.4 - - - +
1407C GLN* 1.3 67.0 + - - +
1408C CYS* 4.2 4.6 + - + -
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Residues in contact with GLN1407 (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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1344C ALA 3.6 0.7 - - - +
1345C VAL* 3.3 4.9 - - - +
1346C GLY* 2.8 37.3 + - - +
1348C TYR* 3.5 28.0 + - + -
1360C VAL* 5.4 1.6 - - - +
1388C MET* 3.0 37.2 - - + +
1390C THR 2.9 28.0 + - - +
1391C THR 3.8 3.1 - - - +
1392C SER 2.9 26.9 + - - +
1393C ALA* 5.0 1.0 - - - -
1394C PRO* 4.5 2.4 - - - +
1405C TYR 4.0 0.6 + - - -
1406C ILE* 1.3 73.6 - - - +
1408C CYS* 1.3 62.9 + - - +
1409C PHE* 3.9 23.8 - - + -
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Residues in contact with CYS1408 (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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1343C PHE* 4.3 3.8 - - - -
1344C ALA 3.1 11.4 - - - +
1345C VAL* 4.1 8.3 - - + -
1371C ARG* 3.5 29.4 - - - -
1374C PHE* 4.0 26.7 - - - -
1375C GLN* 3.9 30.3 + - + +
1378C LEU* 5.2 1.8 - - + -
1388C MET 5.1 3.0 + - - -
1390C THR 5.3 0.2 + - - -
1406C ILE* 4.2 5.5 + - + -
1407C GLN* 1.3 77.9 - - - +
1409C PHE* 1.3 65.4 + - - +
28D PHE* 3.2 21.8 - - - -
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Residues in contact with PHE1409 (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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1343C PHE* 3.5 2.6 - - - -
1344C ALA* 2.8 52.5 + - + -
1346C GLY 5.8 0.9 - - - -
1360C VAL* 5.9 1.8 - - + -
1371C ARG* 3.5 9.6 - - - +
1391C THR* 3.6 28.5 - - + -
1407C GLN* 3.9 33.0 - - + -
1408C CYS* 1.3 81.6 - - - +
1410C THR* 1.3 62.5 + - - +
1411C VAL* 3.8 7.0 - - + -
1444C TYR* 3.4 46.9 - + + -
1469C PHE* 4.0 15.9 - + - -
28D PHE* 3.6 18.8 - - + -
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Residues in contact with THR1410 (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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1341C ASP* 4.3 20.9 - - - +
1342C TYR 3.2 18.4 - - - +
1343C PHE* 3.6 20.8 - - + -
1371C ARG* 3.3 22.4 + - - +
1409C PHE* 1.3 73.2 - - - +
1411C VAL* 1.3 66.5 + - - +
1412C GLN* 4.5 9.0 + - - +
1444C TYR* 3.2 26.2 - - - -
25D THR 5.4 5.4 - - - +
26D ASN* 3.7 15.0 + - + +
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Residues in contact with VAL1411 (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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1341C ASP* 5.5 0.2 - - - +
1342C TYR* 2.7 45.2 + - + +
1344C ALA* 3.9 12.3 - - + +
1362C ILE* 4.1 14.1 - - + -
1409C PHE* 3.6 24.7 + - + -
1410C THR* 1.3 81.0 - - - +
1412C GLN* 1.3 73.1 + - - +
1413C PRO* 3.8 6.2 - - - +
1442C PHE* 3.8 20.0 - - + -
1443C HIS 3.5 13.7 - - - +
1444C TYR* 4.0 2.0 - - + -
1469C PHE* 3.9 18.4 - - + -
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Residues in contact with GLN1412 (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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1341C ASP* 5.4 3.6 + - - -
1410C THR* 4.5 11.5 - - - +
1411C VAL* 1.3 84.4 + - - +
1413C PRO* 1.3 73.6 - - - +
1414C VAL* 4.1 1.1 - - + +
1442C PHE* 3.1 6.4 - - - -
1443C HIS* 2.8 51.0 + - + +
1444C TYR* 6.0 0.7 - - - -
1445C SER 6.3 0.2 - - - +
25D THR 5.9 1.6 + - - -
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Residues in contact with PRO1413 (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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1339C LYS* 6.1 2.2 - - + -
1340C PRO 5.5 1.6 - - - +
1342C TYR* 3.9 34.3 - - + +
1411C VAL 3.8 6.7 - - - +
1412C GLN* 1.3 96.2 - - + +
1414C VAL* 1.3 60.5 + - - +
1415C LEU 4.2 0.3 + - - -
1435C LYS 3.6 21.7 - - - +
1436C SER* 4.1 10.8 - - - +
1439C VAL* 4.1 9.4 - - + -
1441C ARG 3.6 0.2 - - - +
1442C PHE* 3.6 17.2 - - + -
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Residues in contact with VAL1414 (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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1412C GLN* 4.1 3.1 - - + +
1413C PRO* 1.3 77.0 - - - +
1415C LEU* 1.3 75.8 + - - +
1416C ASP* 3.1 4.7 + - - -
1435C LYS 4.5 0.4 - - - -
1439C VAL* 3.4 14.7 - - - +
1440C GLN 5.2 0.2 + - - -
1441C ARG* 2.7 50.5 + - + +
1443C HIS* 3.2 46.0 - - + +
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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