Contacts of the helix formed by residues 1448 - 1457 (chain B) in PDB entry 4ZLP
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 SER1448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1429B GLU* 5.4 1.7 + - - +
1444B PRO 4.8 0.4 + - - -
1445B ALA 5.4 1.5 - - - -
1446B CYS* 3.3 0.6 - - - -
1447B SER* 1.3 79.2 + - - +
1449B PRO* 1.3 73.9 - - - +
1450B ALA* 3.6 7.5 + - - +
1451B CYS* 3.1 33.3 + - - +
1452B LEU 3.3 0.2 + - - -
1453B TYR* 2.9 20.7 + - - -
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Residues in contact with PRO1449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447B SER 4.3 0.7 - - - +
1448B SER* 1.3 87.7 - - - +
1450B ALA* 1.3 54.5 + - - +
1452B LEU* 2.7 31.0 + - - +
1453B TYR* 3.5 41.4 - - + +
1598B ASP* 3.9 23.6 - - + +
1600B CYS 5.2 0.7 - - - +
1601B PHE* 5.5 2.9 - - + -
1602B PRO* 5.2 11.9 - - + -
1606B SER* 5.9 2.6 - - - -
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Residues in contact with ALA1450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B PRO 4.6 4.2 - - - +
1425B TRP* 4.8 0.2 - - - -
1427B GLN* 3.3 40.2 + - + +
1428B CYS* 3.5 18.6 + - - +
1429B GLU* 5.0 1.6 - - + +
1448B SER* 3.3 7.3 + - - +
1449B PRO* 1.3 78.5 - - - +
1451B CYS* 1.3 56.4 + - - +
1452B LEU* 3.2 11.0 + - - +
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Residues in contact with CYS1451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425B TRP* 4.5 9.1 + - - -
1428B CYS* 2.0 51.1 - - - -
1429B GLU* 3.8 7.2 - - - -
1430B ALA* 4.3 4.7 - - - -
1433B CYS* 3.9 10.4 - - - +
1437B PHE* 4.9 1.0 - - - -
1445B ALA 4.5 2.7 - - - -
1446B CYS* 3.3 30.3 - - - +
1448B SER* 3.1 19.9 + - - +
1449B PRO 3.1 0.8 - - - -
1450B ALA* 1.3 75.5 - - - +
1452B LEU* 1.3 72.1 + - - +
1453B TYR 3.1 2.8 + - - -
1454B ASP* 3.4 5.2 + - - -
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Residues in contact with LEU1452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B PRO* 3.5 31.2 - - + +
1425B TRP* 4.0 14.6 - - + +
1437B PHE* 3.9 10.6 - - + -
1449B PRO 2.7 19.0 + - - +
1450B ALA* 4.3 5.6 - - - +
1451B CYS* 1.3 81.1 - - - +
1453B TYR* 1.3 67.0 + - - +
1454B ASP 3.0 6.9 + - - -
1455B ASN* 3.1 12.6 + - - -
1601B PHE* 5.3 3.1 - - + -
1606B SER* 4.3 8.1 - - - +
1609B ASP* 4.1 18.4 - - + +
1610B TYR* 4.1 21.8 - - + +
1613B ALA* 3.5 32.5 - - + -
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Residues in contact with TYR1453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446B CYS 3.6 1.3 - - - -
1447B SER* 3.4 21.9 - - - +
1448B SER 2.9 13.6 + - - -
1449B PRO* 3.5 34.6 - - + +
1451B CYS 3.1 0.2 + - - -
1452B LEU* 1.3 77.4 - - - +
1454B ASP* 1.3 71.1 + - - +
1456B PHE* 2.8 44.5 + + + +
1457B ASP 3.8 1.2 + - - -
1458B CYS* 4.6 2.8 + - - +
1459B HIS* 6.3 1.1 - - + -
1598B ASP* 3.2 42.8 - - + +
1599B HIS* 3.6 14.9 + - + -
1600B CYS 2.3 35.8 + - - -
1601B PHE* 4.0 24.9 - + - -
1602B PRO* 4.8 0.2 - - - +
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Residues in contact with ASP1454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436B LEU* 2.7 19.4 - - - +
1437B PHE* 3.7 7.2 - - - -
1441B ARG 3.2 2.1 - - - +
1442B CYS* 3.8 0.2 - - - -
1443B ASP* 2.7 35.1 + - - +
1446B CYS* 3.0 28.9 + - + +
1447B SER* 4.3 3.8 - - - -
1451B CYS 3.4 4.2 + - - -
1452B LEU 3.0 2.4 + - - -
1453B TYR* 1.3 78.1 - - - +
1455B ASN* 1.3 65.2 + - - +
1457B ASP* 3.0 24.0 + - + +
1458B CYS* 4.2 2.2 - - - -
5002B CA 2.4 30.4 - - - -
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Residues in contact with ASN1455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437B PHE* 3.3 44.9 + - + +
1438B ASN* 5.1 1.4 + - - +
1440B SER 6.1 0.4 - - - +
1452B LEU 3.1 9.4 + - - -
1454B ASP* 1.3 78.2 - - - +
1456B PHE* 1.3 70.9 + - - +
1457B ASP* 3.1 8.4 + - - +
1465B ARG* 3.8 19.0 + - - +
1610B TYR* 2.7 35.7 + - - -
1614B LEU* 3.4 7.2 - - - +
1619B ARG* 3.7 32.1 - - - +
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Residues in contact with PHE1456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453B TYR* 2.8 37.0 + + + +
1455B ASN* 1.3 76.1 - - - +
1457B ASP* 1.3 57.8 + - - +
1458B CYS 3.1 3.1 - - - +
1459B HIS* 3.7 18.4 - + + +
1460B ALA* 2.8 43.3 + - + +
1465B ARG* 4.8 4.3 - - - -
1538B ILE 4.2 2.0 - - - -
1539B LEU 4.2 4.7 - - - -
1540B ARG* 3.5 38.6 - - + -
1599B HIS* 3.3 29.6 - - + -
1601B PHE* 3.9 23.8 - + - -
1610B TYR* 3.3 41.3 - + - -
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Residues in contact with ASP1457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437B PHE 3.6 7.6 - - - +
1439B ASN* 3.2 7.4 - - - +
1440B SER* 3.4 4.5 + - - -
1441B ARG* 3.4 29.4 - - - +
1442B CYS* 3.7 10.8 + - - +
1453B TYR 3.8 0.6 + - - -
1454B ASP* 3.0 26.7 + - - +
1455B ASN* 3.1 7.7 + - - +
1456B PHE* 1.3 78.1 - - - +
1458B CYS* 1.3 60.3 + - - +
1460B ALA 4.1 4.0 - - - -
1461B GLY* 4.3 14.1 + - - -
1465B ARG* 3.0 29.0 + - - +
5002B CA 2.4 25.3 - - - -
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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