Contacts of the helix formed by residues 1453 - 1461 (chain A) in PDB entry 5IY8
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 GLY1453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870A SER* 4.7 3.8 - - - -
882A SER* 4.1 20.7 - - - -
1428A MET* 6.4 0.7 - - - -
1452A LYS* 1.3 80.0 - - - +
1454A VAL* 1.3 61.6 + - - -
1456A GLU* 3.0 26.0 + - - +
1457A ASN* 2.7 28.4 + - - -
1465A PRO* 4.4 2.2 - - - -
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Residues in contact with VAL1454 (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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869A GLU* 4.3 12.1 - - + +
870A SER* 4.3 20.4 - - - +
872A MET* 5.4 2.9 - - - -
1086A MET* 3.6 31.0 - - + -
1453A GLY* 1.3 71.3 - - - +
1455A SER* 1.3 65.7 + - - +
1457A ASN* 3.6 2.3 + - - +
1458A ILE* 3.2 31.1 + - + +
1464A ALA* 4.5 3.7 - - + +
1465A PRO* 4.8 9.2 - - + -
1466A ALA* 4.0 19.1 - - + +
1091B ARG* 5.8 0.9 - - - +
1095B ILE* 4.3 28.5 - - + -
1103B LEU* 5.7 0.9 - - + -
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Residues in contact with SER1455 (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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866A LYS* 3.3 12.2 + - - -
869A GLU* 2.7 35.6 + - - -
1428A MET* 5.0 10.5 - - - -
1431A SER* 4.6 2.7 - - - -
1453A GLY 3.5 0.2 - - - -
1454A VAL* 1.3 77.1 - - - +
1456A GLU* 1.3 71.2 + - - +
1458A ILE* 3.2 3.5 + - - +
1459A MET* 3.0 44.1 + - - +
1091B ARG* 3.5 14.0 + - - +
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Residues in contact with GLU1456 (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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882A SER* 5.4 3.3 - - - -
1424A THR* 5.6 0.7 - - - -
1425A GLY 4.5 9.4 + - - -
1427A LEU* 4.1 13.6 - - + +
1428A MET* 3.9 36.6 - - + +
1449A ASP* 3.9 27.7 - - - +
1450A PRO* 5.7 0.9 - - - +
1451A MET* 3.4 29.7 - - + +
1452A LYS 4.8 2.1 + - - -
1453A GLY* 3.0 37.3 + - - +
1455A SER* 1.3 73.8 + - - +
1457A ASN* 1.3 61.8 + - - +
1459A MET* 3.7 2.8 - - - +
1460A LEU* 3.1 25.6 + - - +
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Residues in contact with ASN1457 (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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1451A MET* 2.7 27.6 + - - +
1453A GLY 2.7 24.2 + - - +
1454A VAL 3.9 2.5 - - - +
1455A SER 3.2 0.4 - - - -
1456A GLU* 1.3 79.0 - - - +
1458A ILE* 1.3 57.1 + - - +
1460A LEU* 3.7 1.5 + - - -
1461A GLY 3.0 19.9 + - - -
1462A GLN* 2.1 60.0 + - + +
1463A LEU 4.5 1.6 - - - +
1464A ALA* 3.9 7.6 - - - -
1465A PRO* 3.4 30.7 - - + +
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Residues in contact with ILE1458 (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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354A LEU 5.7 0.9 - - - +
355A MET* 5.1 6.3 - - + -
357A LYS* 6.0 1.4 - - - -
1454A VAL* 3.2 22.6 + - + +
1455A SER* 3.2 7.8 + - - +
1457A ASN* 1.3 74.9 - - - +
1459A MET* 1.3 66.2 + - + +
1461A GLY* 3.2 13.0 + - - -
1462A GLN 4.8 1.8 - - - +
1464A ALA* 3.8 24.9 - - + +
1091B ARG* 4.7 16.2 - - + +
1095B ILE* 6.0 0.7 - - + -
1100B ALA 5.4 0.4 - - - +
1103B LEU* 3.8 32.5 - - + -
1104B ARG* 4.8 13.0 - - + +
1107B LEU* 3.9 37.7 - - + +
1152B PRO* 5.2 1.9 - - - +
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Residues in contact with MET1459 (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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350A VAL* 4.8 4.9 - - + +
354A LEU* 4.0 38.6 - - + +
355A MET* 3.4 38.6 - - + -
1427A LEU* 4.5 28.3 - - + +
1431A SER* 3.3 34.3 - - - -
1455A SER* 3.0 24.8 + - - +
1456A GLU* 3.7 4.0 - - - +
1458A ILE* 1.3 78.8 - - + +
1460A LEU* 1.3 59.4 + - - +
1461A GLY 3.6 0.2 + - - -
1152B PRO* 3.9 6.8 - - - +
1155B CYS* 3.4 26.0 - - - +
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Residues in contact with LEU1460 (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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18A ILE* 3.5 35.4 - - + -
21A VAL* 5.2 2.7 - - + -
1427A LEU* 5.8 1.7 - - + +
1451A MET* 3.5 24.9 - - - -
1456A GLU 3.1 15.0 + - - +
1457A ASN 4.0 3.6 - - - +
1459A MET* 1.3 78.8 - - - +
1461A GLY* 1.3 59.1 + - - +
1462A GLN* 3.3 33.4 + - + +
1149B VAL* 5.6 2.0 - - + -
1150B ARG 4.0 2.4 - - - +
1151B MET* 3.7 20.8 - - + +
1152B PRO* 3.6 11.1 - - - +
1155B CYS* 4.4 6.1 - - - -
1159B PHE* 5.7 2.7 - - + -
1171B MET* 4.2 16.8 - - + -
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Residues in contact with GLY1461 (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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1457A ASN 3.0 6.8 + - - -
1458A ILE* 3.2 14.8 + - - -
1459A MET 3.2 0.2 - - - -
1460A LEU* 1.3 77.0 - - - +
1462A GLN* 1.3 64.2 + - - +
1104B ARG* 3.2 27.2 - - - +
1107B LEU 5.5 0.4 - - - -
1108B PHE* 4.2 14.9 - - - -
1150B ARG 4.8 5.6 - - - -
1152B PRO* 4.0 14.1 - - - -
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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