Contacts of the helix formed by residues 1057 - 1064 (chain A) in PDB entry 5C53
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 MET1057 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899A ALA* 3.6 35.7 - - + +
902A LEU* 4.8 1.6 - - + -
903A GLY* 3.6 34.1 - - - +
914A THR* 5.5 5.8 - - + -
916A PHE* 3.7 27.8 - - + -
954A ILE* 4.6 4.3 - - + -
1056A GLU* 1.3 86.5 - - - +
1058A PHE* 1.3 68.9 + - + +
1059A ASN* 2.9 18.3 + - - +
1060A LYS* 3.1 17.2 + - + +
1061A LEU* 3.8 26.3 + - + +
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Residues in contact with PHE1058 (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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953A ARG* 4.0 14.8 - - + -
954A ILE* 3.1 48.5 - - + -
988A ALA* 4.3 25.4 - - + -
1052A GLY* 5.8 6.3 - - - +
1056A GLU* 3.5 39.1 - - + -
1057A MET* 1.3 84.4 - - + +
1059A ASN* 1.3 59.4 + - - +
1060A LYS 3.2 0.4 - - - -
1061A LEU* 3.2 20.8 + - + +
1062A GLU* 2.9 43.5 + - + +
1097A VAL* 5.8 0.7 - - + -
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Residues in contact with ASN1059 (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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906A HIS* 5.4 11.2 - - + -
1050A LYS 5.6 1.1 - - - +
1051A GLY* 3.1 9.5 - - - -
1052A GLY* 2.6 48.8 + - - +
1053A THR* 5.4 0.8 - - - +
1056A GLU 4.1 6.5 + - - -
1057A MET* 2.9 16.8 + - - +
1058A PHE* 1.3 80.2 - - - +
1060A LYS* 1.3 56.2 + - - +
1062A GLU* 3.6 9.4 + - - +
1063A SER* 2.9 25.5 + - - -
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Residues in contact with LYS1060 (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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902A LEU* 3.4 52.7 + - + +
905A ALA 5.3 0.8 - - - -
906A HIS* 3.6 42.4 + - + +
1057A MET* 3.1 12.0 + - + +
1059A ASN* 1.3 74.7 - - - +
1061A LEU* 1.3 62.5 + - + +
1062A GLU 3.1 1.6 - - - -
1063A SER* 2.9 24.3 + - - -
1064A ILE* 2.9 46.1 + - + +
1073A PRO* 5.8 2.2 - - - -
1168A LEU* 4.9 13.9 - - - +
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Residues in contact with LEU1061 (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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899A ALA* 5.0 5.6 - - + -
902A LEU* 3.8 32.5 - - + -
954A ILE* 4.3 10.1 - - + -
955A TYR* 5.6 1.3 - - + -
1057A MET* 3.9 32.8 - - + +
1058A PHE* 3.2 21.7 + - + +
1060A LYS* 1.3 79.2 - - + +
1062A GLU* 1.3 60.1 + - - +
1064A ILE* 3.9 5.8 + - - +
1065A ALA* 3.4 19.4 + - - +
1097A VAL* 3.7 43.4 - - + +
1100A VAL* 4.2 16.0 - - + +
1101A VAL* 5.1 7.6 - - + -
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Residues in contact with GLU1062 (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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1050A LYS* 3.0 51.5 + - - +
1051A GLY* 4.5 4.8 - - - -
1052A GLY 5.9 0.7 - - - -
1058A PHE* 2.9 30.0 + - + +
1059A ASN* 3.8 5.6 - - - +
1061A LEU* 1.3 77.7 - - + +
1063A SER* 1.3 57.9 - - - +
1064A ILE 3.2 0.4 - - - -
1065A ALA* 2.9 7.8 + - - +
1066A THR* 2.9 39.2 + - + +
1093A MET* 4.4 16.9 - - + +
1097A VAL* 5.1 7.2 - - + -
1T A 3.9 8.6 + - - -
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Residues in contact with SER1063 (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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906A HIS* 5.5 6.3 + - - -
1059A ASN 2.9 17.5 + - - -
1060A LYS* 2.9 22.8 + - - +
1062A GLU* 1.3 77.4 - - - +
1064A ILE* 1.3 60.8 + - - +
1066A THR* 2.7 20.7 + - - -
1067A SER* 3.4 13.9 + - - -
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Residues in contact with ILE1064 (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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902A LEU* 6.0 0.9 - - + -
1060A LYS* 2.9 44.1 + - + +
1061A LEU* 4.2 1.8 - - + +
1063A SER* 1.3 81.1 - - - +
1065A ALA* 1.3 57.1 + - - +
1066A THR 3.3 1.5 + - - -
1067A SER* 4.1 4.4 + - - +
1071A ARG* 3.2 44.9 + - + +
1073A PRO* 3.7 34.1 - - + -
1096A ARG* 3.3 1.7 + - - -
1099A TRP* 5.4 0.7 + - - -
1100A VAL* 3.7 34.6 - - + +
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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