Contacts of the strand formed by residues 1204 - 1207 (chain C) in PDB entry 1UKJ
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 LEU1204 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096C THR* 3.8 12.1 - - + -
1100C LEU* 3.7 29.2 - - + -
1182C THR* 4.3 2.7 - - + -
1183C VAL 2.9 6.2 + - - +
1184C VAL* 3.4 21.6 - - + -
1185C VAL* 2.9 24.0 + - - +
1198C LEU* 4.0 2.5 - - - -
1202C ALA* 4.3 2.8 - - - +
1203C ASP* 1.3 85.5 - - - +
1205C VAL* 1.3 66.7 + - - +
1206C VAL* 5.7 0.2 - - + -
1224C VAL* 4.2 7.2 - - + -
1225C VAL 3.3 15.7 - - - +
1226C GLY* 4.1 1.3 - - - -
1230C LEU* 3.9 31.2 - - + -
1231C VAL* 4.0 19.1 - - + -
1234C ILE* 4.1 11.9 - - + -
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Residues in contact with VAL1205 (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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1078C GLU* 3.9 20.0 - - - +
1185C VAL 3.2 11.0 - - - +
1187C ASN* 4.1 5.6 - - + -
1197C PRO* 3.6 44.0 - - + -
1198C LEU* 4.1 15.3 - - + +
1204C LEU* 1.3 77.4 - - - +
1206C VAL* 1.3 64.5 + - - +
1207C HIS* 4.5 5.5 - - - +
1223C ILE 3.6 0.9 - - - +
1224C VAL* 3.2 6.1 - - - +
1225C VAL* 3.0 55.1 + - + +
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Residues in contact with VAL1206 (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 ALA* 4.1 10.5 - - + +
1093C ILE* 4.2 18.2 - - + -
1096C THR* 3.9 21.3 - - + +
1155C TYR* 3.8 18.4 - - + +
1184C VAL* 4.0 15.7 - - + -
1185C VAL 3.1 3.6 + - - +
1186C ASP* 3.4 31.9 - - + +
1187C ASN 3.1 23.6 + - - -
1204C LEU* 5.7 0.9 - - + -
1205C VAL* 1.3 78.2 - - - +
1207C HIS* 1.3 64.4 + - - +
1223C ILE 3.2 5.2 - - - +
1224C VAL* 4.1 9.4 - - + -
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Residues in contact with HIS1207 (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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1074C MET* 3.8 16.2 - - + -
1078C GLU* 2.4 34.7 + - + +
1089C GLY* 3.6 5.9 - - - -
1092C ALA* 4.1 1.8 - - - +
1187C ASN* 3.0 39.6 + - + +
1188C THR* 3.7 7.5 + - - -
1191C THR* 4.0 2.4 - - - -
1192C PRO* 3.8 19.0 - - + +
1205C VAL* 4.5 8.5 - - + +
1206C VAL* 1.3 77.1 - - - +
1208C SER* 1.3 59.7 + - - +
1209C ALA 3.4 0.2 - - - -
1211C LLP 6.0 0.4 - - - -
1213C LEU* 3.9 17.5 - - + +
1222C GLY* 3.1 6.4 - - - -
1223C ILE* 2.6 52.1 + - + -
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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