Contacts of the helix formed by residues 110 - 119 (chain C) 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 LYS 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C ASP* 1.3 76.3 - - - +
111C VAL* 1.3 54.6 + - - +
112C ILE* 3.1 14.1 + - - +
113C TYR* 4.0 10.9 + - - +
365D ARG 4.5 6.5 + - - +
366D VAL* 4.1 26.5 - - + +
367D THR 5.4 3.6 - - - +
402D ASP* 4.8 15.0 - - - +
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Residues in contact with VAL 111 (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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99C ASP* 5.1 6.1 - - + +
102C ALA* 4.4 11.0 - - + +
103C ARG* 4.3 30.3 - - + +
109C ASP* 3.3 9.9 + - + +
110C LYS* 1.3 72.7 - - - +
112C ILE* 1.3 53.3 + - - +
113C TYR* 3.0 7.4 - - - -
114C SER* 2.9 30.3 + - - -
227C ALA* 6.0 7.6 - - + -
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Residues in contact with ILE 112 (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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99C ASP* 6.0 4.7 - - - -
109C ASP 4.9 0.4 + - - -
110C LYS* 3.1 6.7 - - - -
111C VAL* 1.3 72.4 - - - +
113C TYR* 1.3 62.6 + - - +
114C SER* 3.1 3.2 + - - -
115C LYS* 3.9 10.6 + - - +
118C ASP* 5.4 4.9 - - - +
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Residues in contact with TYR 113 (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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110C LYS 4.0 10.3 + - - +
111C VAL* 4.4 3.1 - - - +
112C ILE* 1.3 77.4 - - - +
114C SER* 1.3 53.8 + - - +
115C LYS 2.9 22.2 - - - +
118C ASP* 5.5 8.3 - - - +
228C PRO* 5.6 4.6 - - + +
230C MET* 5.6 5.7 - - - +
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Residues in contact with SER 114 (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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98C TYR 5.2 2.7 - - - -
99C ASP* 5.0 14.8 - - - -
102C ALA* 4.7 18.8 - - - -
111C VAL 2.9 16.7 + - - -
112C ILE* 3.1 1.7 - - - -
113C TYR* 1.3 75.1 - - - +
115C LYS* 1.3 56.5 + - - +
228C PRO* 4.4 21.2 - - - +
304O THR* 5.7 1.9 - - - +
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Residues in contact with LYS 115 (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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112C ILE 3.9 7.8 + - - +
113C TYR 2.9 15.4 + - - +
114C SER* 1.3 78.7 - - - +
116C TYR* 1.3 66.2 + - - +
117C THR* 3.3 9.1 + - - +
118C ASP* 4.1 7.3 + - - +
119C LEU* 5.1 2.3 + - - +
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Residues in contact with TYR 116 (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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115C LYS* 1.3 75.2 - - - +
117C THR* 1.3 59.6 + - - +
118C ASP 3.1 6.0 + - - -
119C LEU* 3.4 16.6 + - - +
120C VAL* 4.3 4.3 + - - +
338O GLU* 3.8 24.7 - - + +
339O TRP* 4.6 11.0 - - + +
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Residues in contact with THR 117 (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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115C LYS* 3.3 8.6 - - - +
116C TYR* 1.3 76.7 - - - +
118C ASP* 1.3 59.3 + - - +
119C LEU 3.5 0.9 - - - -
120C VAL* 4.4 13.0 + - - +
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Residues in contact with ASP 118 (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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112C ILE 5.4 7.9 - - - +
113C TYR* 5.5 6.5 - - - +
115C LYS* 4.1 7.8 + - - +
116C TYR 3.1 1.4 + - - -
117C THR* 1.3 77.9 - - - +
119C LEU* 1.3 58.4 + - - +
120C VAL 3.6 3.4 - - - +
404D SER* 5.6 1.7 - - - -
405D PHE* 3.5 22.0 + - - +
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Residues in contact with LEU 119 (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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115C LYS 5.1 0.2 + - - -
116C TYR* 3.4 12.0 + - - +
118C ASP* 1.3 78.3 - - - +
120C VAL* 1.3 61.9 + - - +
121C PRO 4.1 0.2 - - - -
230C MET* 5.5 12.8 - - + +
405D PHE* 4.2 10.7 - - + +
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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