Contacts of the strand formed by residues 1109 - 1113 (chain C) in PDB entry 1X86
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 ILE1109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1028C TRP* 5.0 0.5 + - - -
1076C PHE* 3.7 24.2 - - - -
1098C PHE* 4.0 41.5 - - + -
1100C ILE* 3.9 30.5 - - + +
1107C ALA* 3.8 9.3 + - + +
1108C GLN* 1.3 72.9 - - - +
1110C TYR* 1.3 63.3 + - - +
1111C GLU 3.9 2.3 + - - +
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Residues in contact with TYR1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C TRP* 3.5 39.3 - + - +
1049C LEU* 3.7 17.5 - - + -
1076C PHE* 4.1 10.0 - + + -
1077C SER* 2.9 41.9 + - - -
1079C VAL 4.8 0.5 + - - -
1080C ILE* 3.8 25.1 - - + +
1097C LEU 3.4 0.9 - - - +
1098C PHE* 3.4 2.1 - - - -
1099C VAL* 2.6 55.1 + - + +
1101C SER* 3.9 11.7 - - - -
1108C GLN* 3.8 27.9 + - + -
1109C ILE* 1.3 74.6 - - - +
1111C GLU* 1.3 62.5 + - - +
1112C LEU* 3.5 9.8 + - + -
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Residues in contact with GLU1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C TRP* 2.9 33.3 - - - +
1029C LYS* 3.5 51.1 + - + +
1090C VAL* 4.4 7.8 - - + +
1093C ASP* 4.9 3.6 - - - -
1096C ALA* 4.0 24.5 - - + +
1097C LEU 3.8 2.7 - - - -
1098C PHE* 3.7 34.4 - - + -
1109C ILE* 3.9 4.2 + - + +
1110C TYR* 1.3 71.2 - - - +
1112C LEU* 1.3 62.7 + - - +
1113C VAL* 4.1 1.6 - - + +
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Residues in contact with LEU1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026C LEU* 4.1 34.7 - - + +
1027C VAL 3.3 4.7 - - - +
1028C TRP* 3.6 27.4 - - + -
1038C LEU* 3.8 16.6 - - + -
1047C LEU* 5.2 3.4 - - + -
1049C LEU* 4.2 22.0 - - + -
1095C LYS 4.3 0.5 - - - +
1096C ALA* 3.5 1.2 - - - -
1097C LEU* 2.7 45.9 + - + +
1099C VAL* 3.5 29.6 - - + -
1110C TYR* 4.4 3.1 - - + +
1111C GLU* 1.3 82.3 - - - +
1113C VAL* 1.3 58.6 + - - +
1114C ALA* 3.9 0.9 + - - +
1127C ILE* 6.5 0.2 - - + -
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Residues in contact with VAL1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026C LEU* 3.6 3.2 - - - -
1027C VAL* 2.7 65.8 + - + +
1029C LYS* 4.0 27.4 - - + +
1093C ASP* 4.7 5.6 - - - +
1095C LYS* 4.2 13.2 - - + -
1096C ALA* 3.5 22.9 - - + +
1111C GLU* 5.0 2.5 - - + +
1112C LEU* 1.3 73.9 - - - +
1114C ALA* 1.3 72.8 + - - +
1115C GLN* 5.3 1.3 - - + -
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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