Contacts of the helix formed by residues 115 - 127 (chain C) in PDB entry 2VF7
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 THR 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLY 3.6 0.9 + - - -
112C SER* 3.2 12.1 + - - -
113C VAL 3.2 8.5 + - - -
114C THR* 1.3 79.5 + - - +
116C LEU* 1.3 61.8 + - - +
117C SER 3.4 2.5 - - - -
118C ASN* 3.5 32.3 + - + +
119C LEU* 3.7 18.3 + - + +
359C ARG* 4.8 13.4 + - - +
392C THR* 4.2 10.4 - - - +
395C TYR* 4.8 1.7 - - - -
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Residues in contact with LEU 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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111C GLY 2.9 3.5 + - - +
114C THR* 3.1 33.3 - - - +
115C THR* 1.3 76.2 - - - +
117C SER* 1.3 63.8 + - - +
119C LEU* 3.2 8.0 + - + +
120C LEU* 3.2 25.7 + - + +
317C LEU* 4.4 12.6 - - + -
356C LEU* 4.0 26.1 - - + +
359C ARG* 3.7 35.2 - - + -
360C LEU* 3.7 28.9 - - + +
363C LEU* 4.7 9.4 - - + -
373C LEU* 4.5 12.1 - - + -
395C TYR* 4.6 1.6 - - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 5.0 2.0 + - - -
111C GLY* 2.7 38.0 + - - -
112C SER* 3.9 4.9 + - - -
116C LEU* 1.3 69.9 - - - +
118C ASN* 1.3 65.0 + - - +
120C LEU* 3.5 15.3 + - - +
121C ARG* 3.2 47.6 + - - +
313C SER* 5.2 2.8 + - - -
373C LEU* 4.3 9.6 + - - +
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Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C SER* 5.9 0.2 - - - +
115C THR* 3.5 27.3 + - + +
117C SER* 1.3 79.5 - - - +
119C LEU* 1.3 64.1 + - - +
121C ARG* 3.4 22.9 + - - +
122C MET* 3.1 36.5 + - - +
139C ALA* 5.4 2.3 - - - +
140C GLU* 4.5 12.6 - - - +
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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
----------------------------------------------------------
115C THR* 3.7 25.1 + - + +
116C LEU* 3.2 15.6 + - + +
118C ASN* 1.3 84.2 - - + +
120C LEU* 1.3 57.8 + - - +
122C MET* 3.6 32.4 - - + +
123C LEU* 3.1 21.0 + - - +
352C MET* 5.4 2.3 - - - +
355C ASP* 4.6 14.8 - - - +
356C LEU* 3.8 21.7 - - + +
359C ARG* 3.8 39.7 - - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.2 16.8 + - + +
117C SER* 3.5 19.5 - - - +
119C LEU* 1.3 76.9 - - - +
121C ARG* 1.3 57.8 + - + +
122C MET 3.0 1.3 - - - -
123C LEU* 3.5 9.8 - - + +
124C TYR* 2.8 47.8 + - + -
309C ILE* 3.6 25.1 - - + +
312C LEU* 4.4 19.3 - - + -
313C SER* 4.5 11.9 - - - +
320C VAL* 5.2 9.6 - - + -
324C LEU* 6.4 2.0 - - + -
356C LEU* 4.7 12.3 - - + -
373C LEU* 4.1 23.8 - - + -
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C SER* 5.4 7.5 - - - +
117C SER* 3.2 38.9 + - - +
118C ASN* 3.4 23.7 + - - +
120C LEU* 1.3 81.6 - - + +
122C MET* 1.3 57.2 + - - +
124C TYR* 3.7 2.1 + - - +
125C SER* 3.1 25.1 + - - -
139C ALA* 4.1 4.5 - - + -
140C GLU* 3.1 37.2 + - - +
142C PHE* 3.5 50.7 + - + +
143C SER* 3.8 25.8 + - - +
144C PRO* 5.5 2.6 - - - +
309C ILE* 4.9 4.0 - - + -
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Residues in contact with MET 122 (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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118C ASN* 3.1 22.9 + - - +
119C LEU* 3.6 34.1 - - + +
121C ARG* 1.3 78.7 - - - +
123C LEU* 1.3 64.2 + - - +
125C SER* 3.1 20.4 + - - -
126C ARG* 3.3 7.8 + - - +
139C ALA* 4.3 16.1 - - + +
351C ARG* 4.9 7.4 - - - +
352C MET* 4.1 32.7 - - + +
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Residues in contact with LEU 123 (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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119C LEU 3.1 13.8 + - - +
120C LEU* 3.3 9.8 + - + +
122C MET* 1.3 80.3 - - - +
124C TYR* 1.3 73.2 + - + +
127C ALA* 3.1 30.7 + - + +
304C PHE* 3.6 45.1 - - + -
312C LEU* 6.2 0.4 - - + -
324C LEU* 4.2 18.4 - - + -
349C LEU* 5.2 4.0 - - + +
352C MET* 3.9 18.5 - - + -
353C ALA* 4.5 16.8 - - + +
356C LEU* 3.9 22.9 - - + -
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Residues in contact with TYR 124 (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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120C LEU* 2.8 34.0 + - + +
121C ARG* 4.0 2.7 - - - +
123C LEU* 1.3 79.5 - - + +
125C SER* 1.3 62.0 + - - +
127C ALA 2.8 17.6 - - - +
128C GLY* 4.6 1.9 - - - -
130C TYR* 3.9 11.1 + - - -
142C PHE* 3.7 23.8 - + + -
302C VAL* 3.8 28.4 - - + +
303C THR 4.0 3.6 - - - -
304C PHE* 3.5 28.5 + - + +
307C LEU 2.9 28.1 + - - -
308C ASP 3.7 0.9 - - - -
309C ILE* 3.7 34.5 - - + -
312C LEU* 3.3 40.8 - - + +
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Residues in contact with SER 125 (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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121C ARG 3.1 16.0 + - - -
122C MET* 3.1 15.4 + - - -
124C TYR* 1.3 76.4 - - - +
126C ARG* 1.3 64.1 + - - +
130C TYR* 3.1 20.6 + - - -
136C ILE* 4.2 10.6 - - - +
137C VAL 3.4 11.3 - - - +
138C TYR* 3.2 22.7 - - - +
139C ALA* 3.3 17.1 + - - -
142C PHE* 4.0 1.1 - - - -
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Residues in contact with ARG 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C MET 3.3 4.3 + - - +
125C SER* 1.3 82.0 + - - +
127C ALA* 1.3 65.1 + - - +
128C GLY 5.2 0.2 - - - +
130C TYR* 5.0 3.8 - - - -
342C ARG* 6.0 0.2 + - - -
344C GLU* 4.5 27.3 + - - +
345C GLN* 4.0 12.5 + - - +
348C ALA* 5.2 7.3 - - + +
351C ARG* 4.4 9.4 - - - +
352C MET* 3.6 34.1 - - + -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 3.1 24.3 + - + +
124C TYR 2.8 23.9 - - - +
125C SER 4.0 0.5 - - - +
126C ARG* 1.3 80.8 - - - +
128C GLY* 1.3 61.9 + - - +
130C TYR* 4.3 2.8 - - - -
304C PHE* 4.9 2.7 - - + -
345C GLN* 3.6 18.1 - - + +
348C ALA* 6.0 1.3 - - + +
349C LEU* 3.8 35.9 - - + +
352C MET* 5.2 2.0 - - - -
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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