Contacts of the helix formed by residues 1423 - 1430 (chain N) in PDB entry 4G7Z
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 GLY1423 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1263N PHE 3.4 8.7 - - - -
1264N GLU* 3.3 31.1 + - - -
1265N ALA* 4.1 2.1 - - - +
1375N MET* 4.8 0.2 - - - -
1422N MET* 1.3 76.9 - - - +
1424N VAL* 1.3 66.3 + - - -
1425N THR 3.0 5.1 + - - -
1426N LYS* 3.2 5.1 + - - +
1427N SER* 3.0 20.2 + - - -
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Residues in contact with VAL1424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094N LEU* 5.1 1.1 - - + -
1097N LYS* 4.0 25.4 - - + -
1098N LEU* 4.1 8.3 - - + -
1101N VAL* 3.3 18.7 - - + +
1263N PHE* 3.0 32.9 + - + +
1264N GLU* 3.3 18.8 + - - +
1371N VAL* 3.8 29.4 - - + -
1375N MET* 4.1 6.7 - - + +
1423N GLY* 1.3 70.9 - - - -
1425N THR* 1.3 59.3 + - - +
1427N SER* 4.4 4.5 - - - -
1428N ALA* 3.0 32.6 + - - +
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Residues in contact with THR1425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093N TYR* 5.4 0.4 - - - +
1097N LYS* 3.5 14.2 + - - +
1264N GLU* 2.7 32.5 + - - -
1423N GLY 3.0 1.4 + - - -
1424N VAL* 1.3 76.7 - - - +
1426N LYS* 1.3 66.4 + - - +
1428N ALA 3.4 0.2 + - - -
1429N LEU* 3.0 31.1 + - + +
1440N PHE* 3.6 30.6 - - + -
1441N GLN* 4.0 16.4 - - - +
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Residues in contact with LYS1426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1394N VAL* 5.3 8.8 - - - +
1420N LEU* 6.0 0.8 - - - +
1422N MET* 3.6 39.4 - - + +
1423N GLY* 3.2 8.4 + - - +
1425N THR* 1.3 78.6 - - - +
1427N SER* 1.3 51.8 + - - +
1429N LEU* 3.2 7.4 + - + +
1430N SER* 2.3 50.4 + - - +
19R G 6.5 1.3 - - - -
20R G 3.5 33.8 + - - +
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Residues in contact with SER1427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101N VAL* 4.1 8.0 - - - +
1374N GLN 2.8 28.7 + - - -
1375N MET* 4.7 0.7 - - - -
1377N LYS* 4.1 7.0 + - - -
1378N TYR* 3.0 40.1 + - - -
1422N MET* 4.2 13.3 - - - -
1423N GLY 3.0 18.3 + - - -
1424N VAL* 3.9 5.8 - - - -
1426N LYS* 1.3 78.6 - - - +
1428N ALA* 1.3 60.5 + - - +
1430N SER 3.2 4.0 + - - -
1431N THR* 3.3 4.0 + - - -
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Residues in contact with ALA1428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100N ASP* 3.8 22.9 - - + +
1101N VAL* 3.7 34.7 - - + +
1424N VAL 3.0 19.9 + - - +
1425N THR 4.0 2.9 - - - +
1427N SER* 1.3 76.9 - - - +
1429N LEU* 1.3 58.3 + - - +
1431N THR* 3.2 25.7 - - - +
1437N ALA* 4.2 4.5 - - - -
1440N PHE* 4.2 11.4 - - + -
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Residues in contact with LEU1429 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425N THR* 3.0 22.3 + - + +
1426N LYS* 3.7 7.9 - - + +
1428N ALA* 1.3 76.3 - - - +
1430N SER* 1.3 59.4 + - - +
1431N THR 3.3 4.5 + - - +
1437N ALA* 3.6 31.6 - - - +
1440N PHE* 3.4 20.9 - - + -
1441N GLN* 3.5 31.0 - - + +
1442N ASN* 4.1 23.6 - - + +
1446N VAL* 3.7 17.9 - - + +
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Residues in contact with SER1430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378N TYR* 3.1 36.8 + - - -
1396N GLU* 4.7 0.9 - - - +
1422N MET* 4.2 5.0 - - - +
1426N LYS* 2.3 41.7 + - - +
1427N SER 3.2 0.8 + - - -
1429N LEU* 1.3 77.7 - - - +
1431N THR* 1.3 66.2 + - - +
1432N LYS* 3.5 1.7 + - - -
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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