Contacts of the helix formed by residues 1603 - 1608 (chain A) in PDB entry 5G04
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 LEU1603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1134A TRP* 3.6 31.0 - - + -
1206A ILE* 4.2 7.6 - - + -
1210A LEU* 4.4 1.1 - - + -
1248A ASN* 3.9 12.1 - - - +
1251A VAL* 3.5 32.3 - - + -
1252A ALA* 4.1 19.5 - - + -
1293A SER* 5.1 3.4 - - - +
1297A ALA* 6.5 0.2 - - + -
1593A PRO* 6.2 0.2 - - - -
1599A ASN* 3.8 21.8 + - - +
1602A HIS* 1.3 100.2 - - - +
1604A GLN* 1.3 67.2 + - - +
1605A ALA* 3.5 9.0 + - + +
1606A LEU* 3.6 39.6 + - + +
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Residues in contact with GLN1604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134A TRP* 3.5 39.6 - - + +
1138A HIS* 3.3 29.5 + - + +
1552A TYR* 2.7 39.8 + - - +
1556A LEU* 5.1 2.2 - - + -
1593A PRO* 3.8 22.9 - - + -
1595A HIS 4.4 0.5 - - - +
1596A SER* 4.7 0.8 - - - +
1597A THR 3.8 7.6 + - - -
1598A ASP 3.7 17.3 - - - +
1599A ASN* 3.7 8.9 + - + +
1602A HIS* 4.9 0.2 - - - -
1603A LEU* 1.3 74.2 - - - +
1605A ALA* 1.3 64.4 + - - +
1607A ARG* 3.1 30.1 + - - +
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Residues in contact with ALA1605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134A TRP* 3.6 11.8 - - + -
1137A PHE* 3.9 21.8 - - + -
1138A HIS* 4.5 2.0 - - - -
1177A MET* 3.9 6.8 - - + +
1206A ILE* 3.5 32.8 - - + -
1210A LEU* 4.0 13.7 - - + -
1603A LEU* 3.4 4.4 - - + -
1604A GLN* 1.3 77.4 - - - +
1606A LEU* 1.3 56.5 + - - +
1607A ARG 3.0 5.4 + - - -
1608A HIS* 3.1 23.3 + - - +
1609A LEU 4.5 0.2 + - - -
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Residues in contact with LEU1606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A LEU* 4.4 4.9 - - + +
1255A VAL* 3.4 48.2 - - + -
1296A LEU* 6.1 1.1 - - + -
1297A ALA* 5.4 3.1 - - + -
1300A LEU* 4.9 6.1 - - + -
1586A CYS* 3.8 17.3 - - + +
1587A ALA* 3.7 8.7 + - - -
1602A HIS* 3.5 48.0 - - + +
1603A LEU* 3.6 16.9 + - + +
1604A GLN 3.2 0.6 + - - -
1605A ALA* 1.3 76.5 - - - +
1607A ARG* 1.3 62.2 + - - +
1608A HIS 3.2 0.2 - - - -
1609A LEU* 3.1 45.2 + - + +
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Residues in contact with ARG1607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082A VAL* 3.8 19.1 - - + +
1138A HIS* 4.9 2.0 - - + +
1556A LEU* 3.8 22.2 - - + -
1560A MET* 3.7 26.6 - - - +
1587A ALA* 3.0 34.3 + - - +
1588A LEU 4.5 0.2 - - - -
1589A TYR* 2.8 33.3 + - - +
1591A HIS 3.3 16.2 + - - -
1592A PHE* 3.7 16.7 - - - -
1593A PRO* 3.8 21.4 - - - +
1602A HIS* 3.2 30.0 - - - +
1604A GLN* 3.1 21.2 + - - +
1605A ALA 3.0 0.6 + - - -
1606A LEU* 1.3 77.8 - - - +
1608A HIS* 1.3 56.6 + - - +
1609A LEU 3.2 0.7 + - - -
1610A TYR* 3.2 18.5 - - - -
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Residues in contact with HIS1608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081A PRO 4.7 1.8 - - - -
1082A VAL* 4.0 27.9 - - + +
1085A GLY* 6.0 0.4 - - - -
1137A PHE* 4.3 5.6 - + - -
1138A HIS* 3.2 50.6 - + - -
1141A VAL* 3.5 29.9 - - + +
1142A ALA* 4.5 3.4 - - - -
1145A LEU* 4.0 11.9 - - + +
1177A MET* 4.5 2.2 - - + -
1181A LEU* 3.8 22.0 - - + +
1605A ALA 3.1 16.1 + - - +
1607A ARG* 1.3 71.4 - - - +
1609A LEU* 1.3 65.3 + - - +
1610A TYR* 2.9 18.3 + - + -
1611A VAL* 3.2 21.8 + - - +
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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