Contacts of the helix formed by residues 1431 - 1437 (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 PRO1431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389A ALA* 4.0 13.5 - - + -
1391A ASP* 3.3 47.1 - - - +
1396A LEU* 4.6 3.6 - - + -
1429A ASN 3.7 8.5 - - - +
1430A VAL* 1.4 91.5 - - + +
1432A GLN* 1.3 55.0 + - - +
1433A ILE* 3.4 6.7 - - + -
1434A ILE* 3.0 26.8 + - + -
1435A ARG* 2.8 31.7 + - - +
1464A ILE* 4.0 10.5 - - + -
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Residues in contact with GLN1432 (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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1391A ASP* 4.6 6.1 + - + +
1430A VAL 5.6 0.7 - - - +
1431A PRO* 1.3 68.5 - - - +
1433A ILE* 1.3 64.7 + - + +
1434A ILE 2.8 7.9 + - - -
1435A ARG* 3.1 9.4 + - - +
1436A GLU* 2.7 41.2 + - - +
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Residues in contact with ILE1433 (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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1391A ASP* 3.1 45.1 - - + +
1392A THR* 3.9 4.9 - - - +
1393A MET* 4.3 23.8 - - + +
1396A LEU* 4.5 6.1 - - + -
1431A PRO* 4.1 7.0 - - + -
1432A GLN* 1.3 83.0 - - + +
1434A ILE* 1.3 61.7 + - + +
1436A GLU* 4.3 3.5 - - - +
1437A ASN* 3.6 15.8 + - - +
1457A LEU* 3.6 27.4 - - + +
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Residues in contact with ILE1434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1396A LEU* 3.7 24.2 - - + -
1430A VAL* 3.7 12.1 - - + -
1431A PRO* 3.0 37.9 + - + +
1432A GLN 2.8 1.0 + - - -
1433A ILE* 1.3 80.8 - - + +
1435A ARG* 1.3 65.7 + - - +
1436A GLU 3.2 0.9 - - - -
1437A ASN 3.4 18.2 - - - +
1457A LEU* 3.6 30.1 - - + +
1460A ALA* 4.7 4.0 - - + -
1461A HIS* 3.4 36.0 + - + +
1464A ILE* 4.0 13.2 - - + -
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Residues in contact with ARG1435 (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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1427A ASP 5.8 0.4 - - - +
1430A VAL* 4.5 18.2 - - + +
1431A PRO 2.8 20.3 + - - +
1432A GLN* 3.7 14.1 - - - +
1434A ILE* 1.3 73.6 - - - +
1436A GLU* 1.3 62.5 + - - +
1437A ASN 4.6 1.6 - - - +
1461A HIS* 6.3 0.7 - - - -
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Residues in contact with GLU1436 (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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1432A GLN* 2.7 24.8 + - + +
1433A ILE* 4.4 4.3 - - - +
1435A ARG* 1.3 76.1 - - - +
1437A ASN* 1.3 60.6 + - + +
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Residues in contact with ASN1437 (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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1433A ILE 3.6 8.3 + - - +
1434A ILE* 3.4 20.7 - - - +
1435A ARG 4.6 1.8 - - - +
1436A GLU* 1.3 79.8 - - + +
1452A LEU 6.1 0.4 - - - +
1454A LEU* 5.3 18.7 - - + +
1457A LEU* 3.8 29.2 - - + -
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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