Contacts of the strand formed by residues 1097 - 1100 (chain C) in PDB entry 1AWV
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 ILE1097 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025C PHE* 6.3 0.9 - - + -
1090C LEU* 6.4 0.7 - - + -
1091C LYS 4.3 4.5 - - - +
1092C HIS* 4.1 12.1 - - + -
1093C THR* 3.8 21.8 - - - +
1094C GLY 2.9 34.7 + - - +
1095C PRO 3.4 1.0 + - - +
1096C GLY* 1.3 74.3 - - - +
1098C LEU* 1.3 65.6 + - - +
1099C SER 3.9 0.2 + - - -
1113C PHE 3.6 1.4 - - - +
1114C ILE* 3.2 4.9 - - - -
1115C CYS* 2.8 45.8 + - + +
1128C VAL* 3.4 28.9 - - + -
1130C GLY 3.8 3.1 - - - +
1131C LYS* 4.3 18.4 - - + +
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Residues in contact with LEU1098 (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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1022C PHE* 4.2 19.1 - - + -
1024C LEU* 3.7 20.9 - - + -
1036C PHE* 3.9 16.4 - - + -
1096C GLY 3.4 2.6 + - - +
1097C ILE* 1.3 73.1 - - - +
1099C SER* 1.3 58.8 + - - +
1112C PHE* 3.7 30.3 - - + -
1113C PHE 3.6 5.8 - - - +
1114C ILE* 4.1 11.4 - - + +
1128C VAL* 3.3 4.5 - - - +
1129C PHE* 3.1 58.4 + - + -
1130C GLY* 2.6 26.3 + - - +
1131C LYS* 3.9 3.4 - - - +
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Residues in contact with SER1099 (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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1092C HIS* 3.1 27.3 + - - -
1097C ILE* 3.9 2.9 + - - -
1098C LEU* 1.3 75.1 - - - +
1100C MET* 1.3 67.2 + - - +
1112C PHE* 3.4 6.1 - - - +
1113C PHE* 3.0 52.1 + - - +
1126C HIS* 3.5 8.7 - - - +
1127C VAL 3.0 18.7 + - - -
1128C VAL* 4.0 5.2 - - - -
1129C PHE* 3.4 7.0 - - - -
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Residues in contact with MET1100 (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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1032C THR* 3.5 21.5 - - + +
1035C ASN* 3.9 24.0 - - - +
1036C PHE* 5.5 2.2 - - - -
1048C TYR* 5.6 0.7 - - - -
1083C PHE* 4.3 3.6 - - + -
1099C SER* 1.3 71.9 + - - +
1101C ALA* 1.3 63.2 + - - +
1102C ASN* 4.2 1.4 + - - -
1108C ASN* 3.4 42.6 - - + +
1109C GLY 4.0 13.2 - - - +
1110C SER* 4.7 3.4 - - - +
1111C GLN 3.7 17.0 - - - +
1112C PHE* 4.5 3.4 - - - -
1113C PHE* 3.5 1.9 - - - -
1126C HIS* 2.8 29.3 + - - +
1127C VAL* 2.8 20.2 + - + +
1129C PHE* 3.4 27.4 - - + -
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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