Contacts of the helix formed by residues 1107 - 1114 (chain U) in PDB entry 6FF7
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 MET1107 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442U GLU* 5.4 5.8 - - + +
1104U ILE* 4.3 7.9 - - - +
1105U LYS 3.9 4.0 + - - -
1106U ASN* 1.3 68.5 - - - +
1108U ALA* 1.3 60.1 + - - +
1109U PHE 3.2 0.7 - - - -
1110U GLN* 3.2 14.3 + - + +
1111U LYS* 2.9 27.5 + - - +
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Residues in contact with ALA1108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440U PRO* 3.9 15.9 - - + +
441U THR 3.6 25.1 - - - +
442U GLU* 5.1 3.9 + - - +
444U TYR* 3.6 21.5 - - + +
1106U ASN* 2.9 6.0 + - + +
1107U MET* 1.3 78.1 - - - +
1109U PHE* 1.3 56.8 + - - +
1111U LYS* 3.8 7.6 - - - +
1112U TYR* 3.0 31.9 + - - +
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Residues in contact with PHE1109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472U LEU* 5.9 0.9 - - + +
476U GLU* 4.8 20.0 - - + -
1104U ILE* 5.4 4.3 - - + -
1106U ASN* 3.1 15.5 + - + +
1108U ALA* 1.3 75.8 - - - +
1110U GLN* 1.3 59.5 + - - +
1112U TYR* 5.4 0.4 - - - -
1113U SER* 3.1 32.7 + - - -
1115U MET* 3.2 22.8 + - + +
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Residues in contact with GLN1110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104U ILE* 4.9 8.2 - - + +
1106U ASN 4.2 1.2 + - - -
1107U MET* 3.2 19.0 + - + +
1109U PHE* 1.3 78.4 - - - +
1111U LYS* 1.3 63.8 + - - +
1114U ASN* 2.9 27.5 + - - +
1115U MET* 4.0 5.8 - - - +
1116U GLU* 4.7 18.8 - - + +
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Residues in contact with LYS1111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U PHE 4.9 7.8 - - - +
103U ARG* 4.9 14.5 - - - +
105U ASN* 6.2 3.6 - - - -
444U TYR* 5.5 6.3 - - + +
445U SER 5.9 1.3 - - - +
446U GLY* 5.7 9.0 - - - -
1107U MET 2.9 16.6 + - - +
1108U ALA* 3.4 7.8 + - - +
1110U GLN* 1.3 79.1 - - - +
1112U TYR* 1.3 60.5 + - - +
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Residues in contact with TYR1112 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449U CYS* 6.4 0.2 - - - -
450U LEU* 4.9 20.4 - - + +
452U LEU* 5.6 4.9 - - + -
454U LYS* 4.8 6.8 - - - +
1108U ALA 3.0 15.8 + - - +
1109U PHE* 5.4 0.7 - - - -
1111U LYS* 1.3 78.1 - - + +
1113U SER* 1.3 63.2 + - - +
1114U ASN 3.7 0.4 - - - -
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Residues in contact with SER1113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452U LEU* 4.8 8.3 - - - -
453U PRO 3.2 25.4 - - - -
454U LYS* 4.3 4.0 - - - +
455U LEU* 2.9 27.5 + - - +
472U LEU* 5.8 5.4 - - - -
1109U PHE* 3.1 19.4 + - - -
1112U TYR* 1.3 81.1 - - - +
1114U ASN* 1.3 67.6 + - - +
1115U MET* 3.3 8.1 + - - -
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Residues in contact with ASN1114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455U LEU* 3.4 25.0 - - - +
1109U PHE 3.3 0.2 + - - -
1110U GLN* 2.9 20.5 + - - +
1112U TYR 3.7 1.0 - - - +
1113U SER* 1.3 80.1 - - - +
1115U MET* 1.3 63.4 + - - +
1116U GLU* 3.1 4.8 + - - -
1117U GLN* 3.2 23.2 + - + +
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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