Contacts of the strand formed by residues 1233 - 1235 (chain C) in PDB entry 7C17
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 LEU1233 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C MET 5.4 0.2 - - - +
686C GLN* 3.8 33.4 - - + +
689C ALA* 3.8 30.1 - - + -
796C LEU* 3.7 23.1 - - + +
797C GLY* 3.4 27.1 - - - +
828C PHE* 4.2 1.1 - - - -
1066C MET* 3.4 9.0 - - - +
1067C ALA 2.6 37.9 + - - +
1068C GLY 4.2 4.3 - - - +
1069C ARG* 4.1 2.5 - - - +
1231C TYR* 3.4 28.7 - - + +
1232C MET* 1.3 75.3 - - - +
1234C LYS* 1.3 63.3 + - - +
1235C LEU* 3.7 3.6 + - + +
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Residues in contact with LYS1234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689C ALA* 3.3 4.0 - - - +
690C VAL* 2.5 51.8 + - + +
691C PRO 4.8 0.7 - - - +
692C THR* 4.9 3.6 - - + -
797C GLY* 5.0 2.6 - - - -
828C PHE* 2.4 62.2 + - + +
830C THR* 3.9 16.7 + - - +
1058C ARG 4.4 1.6 + - - -
1059C ARG 4.1 2.6 + - - -
1060C ILE* 3.9 16.1 - - - +
1064C ASP* 3.3 39.1 + - - +
1065C LYS 3.9 2.7 - - - +
1066C MET* 4.4 7.9 - - - +
1233C LEU* 1.3 71.8 - - - +
1235C LEU* 1.3 66.7 + - - +
1238C LEU* 4.3 7.2 - - + +
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Residues in contact with LEU1235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685C MET* 3.3 40.4 - - + +
688C GLN* 3.3 24.2 - - + +
689C ALA* 5.0 2.0 - - + -
690C VAL* 3.5 9.3 - - - +
1065C LYS* 3.2 48.3 + - + +
1066C MET* 4.1 2.5 - - - -
1067C ALA* 3.5 41.1 - - + +
1233C LEU* 3.7 6.5 - - + +
1234C LYS* 1.3 79.4 - - - +
1236C ASN* 1.3 59.5 + - - +
1237C HIS* 3.4 5.2 - - + +
1238C LEU* 3.3 20.8 - - - +
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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
------------------------------------------------------------
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