Contacts of the strand formed by residues 1462 - 1475 (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 MET1462 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1447C PRO* 4.1 19.5 - - + -
1448C VAL 4.3 3.4 - - - +
1449C ARG* 4.0 21.8 - - + +
1458C GLU* 3.6 14.2 + - - +
1459C PHE* 3.7 23.2 + - + +
1460C ALA 3.6 3.2 - - - -
1461C SER* 1.3 76.8 - - - +
1463C TRP* 1.3 67.4 + - - +
1464C ILE* 4.3 1.7 + - + -
1493C SER 4.4 0.3 - - - -
1494C PRO* 3.4 24.9 - - - +
1497C ASN* 3.4 34.1 + - - +
33D ILE* 4.3 5.8 - - + -
34D PRO* 3.7 40.6 - - + +
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Residues in contact with TRP1463 (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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1447C PRO* 3.4 5.4 - - - +
1448C VAL* 2.9 47.2 + - + +
1450C ARG* 3.7 54.1 + - + +
1461C SER* 3.8 11.6 - - - +
1462C MET* 1.3 76.4 - - - +
1464C ILE* 1.3 62.6 + - - +
1491C THR* 4.1 20.6 - - + -
1492C ILE 3.2 24.5 - - - -
1493C SER* 3.3 26.0 - - - -
1494C PRO* 3.4 23.4 - - + +
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Residues in contact with ILE1464 (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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1445C SER* 3.5 30.7 - - - +
1446C ARG 3.7 2.2 - - - +
1447C PRO* 4.0 7.9 - - + -
1448C VAL* 4.7 0.7 - - - -
1462C MET* 4.8 3.6 - - + +
1463C TRP* 1.3 81.3 - - - +
1465C GLU* 1.3 66.5 + - - +
1466C ARG* 4.3 6.7 - - - +
1491C THR* 3.5 6.9 - - - +
1492C ILE* 2.8 54.2 + - + +
1497C ASN* 3.6 36.8 - - + +
33D ILE* 3.4 37.7 - - + -
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Residues in contact with GLU1465 (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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1444C TYR* 3.3 4.7 - - - +
1445C SER* 3.4 0.3 - - - -
1446C ARG* 2.8 72.8 + - - +
1448C VAL* 4.0 19.9 - - + +
1450C ARG* 4.9 4.4 + - - +
1464C ILE* 1.3 72.1 - - - +
1466C ARG* 1.3 60.7 + - - +
1467C THR* 4.0 1.4 + - - -
1489C GLN* 3.2 35.8 - - - +
1490C THR 3.6 2.2 - - - +
1491C THR* 3.6 23.2 + - + +
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Residues in contact with ARG1466 (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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1443C HIS* 3.9 34.9 - - + +
1444C TYR 3.2 9.4 - - - +
1445C SER* 3.0 23.5 + - - +
1464C ILE* 3.8 9.6 + - + +
1465C GLU* 1.3 73.1 + - - +
1467C THR* 1.3 69.3 + - - +
1468C SER* 4.0 1.9 + - - +
1489C GLN* 3.6 4.6 - - - -
1490C THR* 2.9 48.4 + - - +
1492C ILE* 3.6 28.5 - - + +
1497C ASN* 5.1 4.2 + - - -
1500C GLU* 2.7 42.1 + - - -
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Residues in contact with THR1467 (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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1442C PHE 3.6 0.3 - - - +
1443C HIS* 3.2 7.6 + - - -
1444C TYR* 2.9 38.8 + - - +
1446C ARG* 5.1 5.7 + - - -
1465C GLU 4.8 1.2 + - - -
1466C ARG* 1.3 74.5 - - - +
1468C SER* 1.3 63.5 + - - +
1469C PHE* 3.5 30.8 - - + -
1487C MET* 3.8 19.1 - - + -
1488C SER 3.4 12.8 - - - +
1489C GLN* 2.4 34.4 + - - +
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Residues in contact with SER1468 (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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1441C ARG* 4.0 20.8 + - - -
1442C PHE 3.3 4.5 - - - -
1443C HIS* 3.0 29.1 + - - -
1466C ARG* 4.0 2.7 + - - +
1467C THR* 1.3 72.3 - - - +
1469C PHE* 1.3 60.7 + - - +
1470C VAL* 5.4 0.7 - - - -
1486C HIS* 5.5 1.5 - - - -
1487C MET* 3.0 9.5 - - - +
1488C SER* 2.9 49.0 + - - -
1490C THR* 5.6 1.6 + - - -
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Residues in contact with PHE1469 (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* 4.9 1.3 - - + -
1360C VAL* 4.7 9.2 - - + -
1362C ILE* 4.2 18.8 - - + -
1409C PHE* 4.0 27.6 - + - -
1411C VAL* 3.9 13.2 - - + -
1440C GLN 3.8 0.4 - - - +
1441C ARG* 3.4 5.5 - - - +
1442C PHE* 2.8 49.8 + - + +
1444C TYR* 3.8 15.5 - - + -
1467C THR* 3.5 35.0 - - + -
1468C SER* 1.3 74.5 - - - +
1470C VAL* 1.3 63.4 + - - +
1484C VAL* 4.0 15.3 - - + -
1486C HIS 3.8 3.8 - - - -
1487C MET* 3.4 34.3 - - + -
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Residues in contact with VAL1470 (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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1440C GLN* 3.3 20.9 - - + +
1441C ARG* 3.7 37.0 - - + +
1468C SER 5.4 0.9 - - - -
1469C PHE* 1.3 79.4 - - - +
1471C THR* 1.3 73.9 + - - +
1484C VAL* 3.6 2.3 - - - +
1485C VAL* 2.8 35.3 + - + +
1486C HIS* 2.9 36.4 + - + +
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Residues in contact with THR1471 (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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1362C ILE* 3.4 40.6 - - + +
1439C VAL 4.2 0.7 + - - -
1440C GLN* 2.9 37.1 + - - -
1442C PHE* 3.7 10.8 - - + -
1470C VAL* 1.3 80.2 - - - +
1472C ALA* 1.3 69.2 + - - +
1473C TYR 2.9 22.8 + - - -
1475C LEU* 5.2 2.5 - - + +
1482C PHE* 3.9 12.1 - - + +
1483C GLU 3.2 13.9 - - - +
1484C VAL* 4.6 0.4 - - + -
1485C VAL* 4.5 2.8 - - - +
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Residues in contact with ALA1472 (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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1440C GLN* 2.9 17.3 + - - -
1470C VAL 4.1 0.2 + - - -
1471C THR* 1.3 71.0 - - - +
1473C TYR* 1.3 87.4 + - + +
1482C PHE* 4.6 7.1 - - + +
1483C GLU* 3.0 19.1 + - + +
1485C VAL* 4.2 20.4 - - + +
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Residues in contact with TYR1473 (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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1440C GLN* 3.8 4.0 - - - +
1471C THR* 2.9 19.2 + - - -
1472C ALA* 1.3 97.3 - - + +
1474C LYS* 1.3 71.7 + - - +
1475C LEU* 4.8 0.2 - - - +
1478C ILE* 6.3 2.9 - - + -
1482C PHE* 3.4 42.1 - + + +
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Residues in contact with LYS1474 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1416C ASP* 3.0 29.0 + - - -
1418C HIS* 5.4 4.3 - - - -
1438C TYR* 4.1 21.8 - - + +
1439C VAL 3.3 19.3 - - - +
1440C GLN* 3.3 29.7 + - + +
1473C TYR* 1.3 79.7 - - - +
1475C LEU* 1.3 61.6 + - - +
1476C PRO 3.5 9.4 - - - +
1477C GLY* 4.2 1.0 - - - -
1482C PHE* 3.0 17.7 - - - -
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Residues in contact with LEU1475 (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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1342C TYR* 3.8 37.4 + - + -
1362C ILE* 3.6 24.9 - - + +
1364C ARG* 4.0 13.2 - - + +
1437C ASN 3.9 0.2 - - - -
1438C TYR* 2.8 23.8 + - - -
1439C VAL* 3.0 15.8 + - - +
1442C PHE* 4.2 12.6 - - + -
1471C THR* 5.2 2.5 - - + +
1473C TYR 4.8 0.9 - - - +
1474C LYS* 1.3 74.2 - - - +
1476C PRO* 1.3 69.3 - - + +
1479C LEU 3.7 18.2 - - - +
1480C ARG* 3.7 15.5 - - - +
1481C TRP* 4.1 0.7 - - - +
1482C PHE* 3.5 26.9 - - + +
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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