Contacts of the helix formed by residues 135 - 144 (chain V) 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 GLY 135 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23V ILE* 5.4 5.6 - - - +
132V VAL* 5.3 6.6 - - - +
133V CYS 4.2 0.2 + - - -
134V GLN* 1.3 75.4 - - - +
136V ILE* 1.3 65.8 + - - +
137V GLY 3.2 3.4 - - - -
138V MET* 3.2 24.4 + - - +
139V VAL* 3.3 12.6 + - - +
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Residues in contact with ILE 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V GLY* 6.6 0.7 - - - -
132V VAL* 5.6 9.3 - - + +
133V CYS 5.4 3.5 + - - +
135V GLY* 1.3 76.2 - - - +
137V GLY* 1.3 58.2 + - - +
139V VAL* 3.5 5.5 + - - +
140V ASN* 3.0 28.5 + - - +
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Residues in contact with GLY 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135V GLY* 3.2 1.4 - - - -
136V ILE* 1.3 78.1 - - - +
138V MET* 1.3 58.1 + - - +
140V ASN* 3.7 7.6 - - - +
141V ARG* 2.9 28.4 + - - +
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Residues in contact with MET 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V MET* 5.2 13.6 - - + +
21V GLY* 5.9 7.0 - - - +
22V ILE 6.0 1.6 - - - +
23V ILE* 5.4 9.4 - - + -
135V GLY* 3.2 20.5 + - - +
137V GLY* 1.3 76.6 - - - +
139V VAL* 1.3 57.9 + - - +
141V ARG* 3.2 7.7 + - - +
142V VAL* 2.9 26.7 + - - +
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Residues in contact with VAL 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V GLY* 6.4 2.7 - - - -
135V GLY 3.3 10.5 + - - +
136V ILE* 3.5 4.9 + - - +
137V GLY 3.4 0.2 - - - -
138V MET* 1.3 75.9 - - - +
140V ASN* 1.3 60.2 + - - +
142V VAL* 3.8 9.1 - - + +
143V GLY* 2.9 23.9 + - - -
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Residues in contact with ASN 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136V ILE 3.0 19.3 + - - +
137V GLY* 3.7 8.5 - - - +
139V VAL* 1.3 77.9 - - - +
141V ARG* 1.3 60.6 + - - +
143V GLY* 3.5 2.8 + - - +
144V MET* 3.4 20.8 + - - +
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Residues in contact with ARG 141 (chain V).
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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90C VAL 5.8 0.2 - - - +
20V MET* 6.2 2.9 - - + -
137V GLY 2.9 17.6 + - - +
138V MET* 3.2 8.5 + - - +
140V ASN* 1.3 75.0 - - - +
142V VAL* 1.3 64.0 + - - +
144V MET* 3.4 16.4 + - - +
145V VAL* 4.0 4.2 + - - +
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Residues in contact with VAL 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V MET* 5.4 9.0 - - + -
56V ILE* 4.5 8.5 - - - +
138V MET 2.9 15.6 + - - +
139V VAL* 3.8 10.1 - - + +
140V ASN 3.4 0.2 - - - -
141V ARG* 1.3 75.2 - - - +
143V GLY* 1.3 61.4 + - - +
144V MET 3.3 1.0 + - - -
145V VAL* 3.3 20.7 + - - +
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Residues in contact with GLY 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V ILE* 5.2 7.3 - - - +
57V ILE 4.5 8.1 - - - +
58V LYS* 3.9 25.3 + - - +
59V ASP 6.2 0.4 - - - -
62V ILE* 5.5 7.4 - - - -
139V VAL 2.9 17.2 + - - -
140V ASN* 3.5 4.0 + - - -
141V ARG 3.3 0.6 - - - -
142V VAL* 1.3 77.9 - - - +
144V MET* 1.3 56.4 + - - +
145V VAL 3.3 6.5 + - - +
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Residues in contact with MET 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ALA* 4.8 14.5 - - + +
88C ILE 4.3 20.1 - - - +
89C GLN* 5.8 0.3 - - - -
58V LYS* 5.8 1.8 - - - -
140V ASN 3.4 13.4 + - - +
141V ARG* 3.4 10.4 + - - +
142V VAL 3.2 1.6 - - - -
143V GLY* 1.3 75.1 - - - +
145V VAL* 1.3 63.2 + - - +
146V GLU* 3.5 2.9 + - - +
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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