Contacts of the strand formed by residues 1439 - 1449 (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 VAL1439 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1342C TYR* 3.7 31.4 - - + +
1413C PRO* 4.1 14.4 - - + -
1414C VAL 3.4 25.1 - - - +
1416C ASP* 4.3 6.5 - - - +
1434C TYR 3.7 20.6 - - - +
1435C LYS 4.2 6.1 - - - +
1437C ASN* 3.7 8.7 - - - +
1438C TYR* 1.3 77.8 - - - +
1440C GLN* 1.3 60.5 + - - +
1441C ARG 4.5 2.9 - - - +
1442C PHE* 3.9 14.3 - - + -
1471C THR* 4.2 1.0 + - - -
1474C LYS* 3.3 5.2 - - - -
1475C LEU 3.0 27.4 + - - +
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Residues in contact with GLN1440 (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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1416C ASP* 4.7 13.1 - - - +
1439C VAL* 1.3 72.5 - - - +
1441C ARG* 1.3 60.7 + - + +
1442C PHE* 3.6 7.9 - - - -
1470C VAL* 3.3 14.6 - - + +
1471C THR* 2.9 44.9 + - - +
1472C ALA 2.9 26.3 + - - -
1473C TYR* 3.8 1.8 - - - +
1474C LYS* 3.3 46.5 + - + +
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Residues in contact with ARG1441 (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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1413C PRO* 3.6 0.3 - - - +
1414C VAL* 2.7 63.5 + - + +
1416C ASP* 6.1 0.9 - - - +
1439C VAL* 3.7 2.7 - - - +
1440C GLN* 1.3 81.6 - - + +
1442C PHE* 1.3 70.7 + - - +
1443C HIS* 4.6 7.5 - - + -
1468C SER* 4.0 23.2 + - - +
1469C PHE 3.4 7.9 - - - +
1470C VAL* 3.7 23.4 - - + +
1486C HIS* 5.0 9.5 - - - -
1488C SER* 5.6 0.6 + - - -
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Residues in contact with PHE1442 (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* 3.6 32.5 - + + -
1362C ILE* 3.8 29.6 - - + -
1411C VAL* 3.8 21.5 - - + -
1412C GLN 3.1 7.0 - - - +
1413C PRO* 3.6 23.3 - - + -
1414C VAL* 4.2 0.2 - - - -
1439C VAL* 3.9 22.0 - - + -
1440C GLN 3.6 21.3 - - - -
1441C ARG* 1.3 79.5 - - - +
1443C HIS* 1.3 65.2 + - - +
1468C SER* 3.3 5.4 - - - -
1469C PHE* 2.8 45.1 + - + +
1471C THR* 3.7 18.6 - - + -
1475C LEU* 4.2 6.7 - - + -
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Residues in contact with HIS1443 (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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1411C VAL* 3.5 7.5 - - - +
1412C GLN* 2.8 42.8 + - + +
1414C VAL* 3.2 32.5 - - + +
1441C ARG* 4.6 10.5 - - - -
1442C PHE* 1.3 74.3 + - - +
1444C TYR* 1.3 61.2 + - - +
1445C SER* 5.1 1.1 - - - +
1466C ARG* 3.9 31.2 - - + +
1467C THR 3.2 4.7 + - - +
1468C SER* 3.0 29.4 + - - -
1469C PHE* 4.4 0.2 - - - -
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Residues in contact with TYR1444 (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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1391C THR* 3.7 19.5 - - + -
1409C PHE* 3.4 25.1 - + + -
1410C THR 3.2 27.8 - - - -
1411C VAL* 4.0 0.7 - - + -
1412C GLN* 6.0 0.4 - - - -
1443C HIS* 1.3 74.6 - - - +
1445C SER* 1.3 73.8 + - - +
1446C ARG* 3.9 18.2 - - + -
1465C GLU 3.3 2.5 - - - +
1466C ARG* 3.2 6.3 - - - +
1467C THR* 2.9 37.4 + - - +
1469C PHE* 3.8 20.4 - - + -
28D PHE* 3.3 23.7 + - + +
31D GLU* 2.5 35.3 + - - +
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Residues in contact with SER1445 (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* 6.3 0.4 - - - +
1443C HIS* 5.1 1.6 - - - +
1444C TYR* 1.3 87.4 + - - +
1446C ARG* 1.3 60.6 + - - +
1447C PRO* 4.1 2.1 - - - +
1464C ILE* 3.5 17.0 - - - +
1465C GLU 3.4 3.4 - - - -
1466C ARG* 3.0 35.6 + - - +
31D GLU 4.4 3.1 - - - +
33D ILE* 3.6 24.7 - - - +
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Residues in contact with ARG1446 (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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1391C THR* 3.8 12.0 + - - -
1392C SER* 4.3 27.0 + - - +
1444C TYR* 3.9 10.2 - - + -
1445C SER* 1.3 73.0 - - - +
1447C PRO* 1.3 79.5 - - + +
1448C VAL* 3.4 14.5 + - - +
1464C ILE* 4.6 1.3 - - - -
1465C GLU* 2.8 71.7 + - - +
1467C THR* 5.1 4.0 + - - -
1489C GLN* 4.9 7.5 + - - -
31D GLU* 3.2 37.7 - - + +
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Residues in contact with PRO1447 (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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1445C SER 4.1 0.4 - - - -
1446C ARG* 1.3 91.8 - - + +
1448C VAL* 1.3 63.2 + - - +
1449C ARG* 5.8 2.9 - - + +
1462C MET* 4.1 24.2 - - + -
1463C TRP 3.4 7.4 - - - +
1464C ILE* 4.0 4.5 - - + -
30D GLY 4.9 3.1 - - - +
31D GLU* 3.3 28.5 - - + +
32D TYR 3.6 21.3 - - - +
33D ILE* 3.8 17.6 - - + -
34D PRO* 5.6 0.2 - - + -
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Residues in contact with VAL1448 (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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1446C ARG* 3.4 30.5 + - - +
1447C PRO* 1.3 79.1 - - - +
1449C ARG* 1.3 63.7 + - - +
1450C ARG* 4.8 13.7 - - + +
1462C MET* 5.1 0.9 - - - -
1463C TRP* 2.9 52.3 + - + +
1464C ILE 4.7 0.7 - - - -
1465C GLU* 4.0 23.1 - - + +
1491C THR* 5.1 2.0 - - + -
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Residues in contact with ARG1449 (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* 5.8 3.5 - - + +
1448C VAL* 1.3 76.3 - - - +
1450C ARG* 1.3 66.9 + - - +
1451C GLY 5.7 0.7 - - - +
1453C VAL* 3.7 31.7 - - + +
1458C GLU* 3.2 43.7 + - - +
1461C SER* 3.7 17.2 + - - +
1462C MET* 4.0 26.3 - - + +
34D PRO* 4.8 3.2 - - - +
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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