Contacts of the strand formed by residues 1199 - 1203 (chain F) in PDB entry 6X34
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 VAL1199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831F ARG* 4.6 11.4 - - - +
838F HIS* 5.7 1.6 - - + +
839F LEU 3.6 5.4 - - - -
840F VAL* 3.8 21.1 - - + -
1095F VAL* 2.8 38.9 + - + -
1096F THR* 2.8 18.5 + - + +
1100F MET* 3.3 12.2 - - - +
1198F GLN* 1.3 75.9 - - - +
1200F GLY* 1.3 58.5 + - - +
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Residues in contact with GLY1200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838F HIS* 3.4 2.9 - - - +
839F LEU* 2.5 48.0 + - - -
1092F PHE* 4.3 8.7 - - - -
1094F ALA* 3.9 6.7 - - - -
1095F VAL* 3.7 13.9 - - - -
1100F MET* 4.0 8.1 - - - +
1199F VAL* 1.3 77.0 - - - +
1201F HIS* 1.3 56.5 + - - -
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Residues in contact with HIS1201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835F ARG* 4.6 23.0 + - - +
836F GLY* 3.6 29.1 + - - -
837F PRO* 2.6 31.8 + - + -
838F HIS* 3.4 20.6 - + + +
1092F PHE* 3.2 20.3 - - - -
1093F GLU* 2.9 38.2 + - + +
1095F VAL* 4.8 2.7 - - + -
1200F GLY* 1.3 74.3 - - - -
1202F LEU* 1.3 77.9 + - - +
1203F ASN* 4.2 22.3 + - + +
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Residues in contact with LEU1202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837F PRO* 4.1 10.2 + - - +
839F LEU* 3.8 21.1 - - + +
1090F PHE* 5.0 3.6 - - + -
1091F GLU 4.5 0.2 - - - -
1092F PHE* 4.2 5.2 - - + -
1192F CYS* 3.7 26.5 - - - -
1200F GLY 4.3 0.8 + - - -
1201F HIS* 1.3 88.5 + - - +
1203F ASN* 1.3 60.8 + - - +
1204F LEU 4.1 1.2 + - - -
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Residues in contact with ASN1203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089F TYR 5.2 1.0 - - - +
1090F PHE* 3.8 13.5 - - - -
1091F GLU* 3.1 50.8 + - + +
1092F PHE* 5.4 0.2 - - - -
1201F HIS* 4.0 21.4 + - + +
1202F LEU* 1.3 73.8 - - - +
1204F LEU* 1.3 60.9 + - - +
1205F GLY* 3.0 22.8 + - - +
1210F SER* 3.1 42.4 + - - +
1211F LEU* 4.7 3.5 - - - +
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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