Contacts of the helix formed by residues 128 - 144 (chain C) in PDB entry 2V1C
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 ASP 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLN* 3.1 5.3 + - + +
127C PRO* 1.3 78.6 - - + +
129C PRO* 1.3 64.4 - - - +
130C GLU* 3.6 4.9 + - - +
131C TRP* 3.3 25.4 + - + +
132C VAL* 3.3 17.7 + - - +
205C PRO* 5.1 3.7 - - + +
211C ARG* 2.7 41.9 + - - -
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Residues in contact with PRO 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU* 4.2 18.4 - - - +
88C ARG* 3.8 43.5 - - + +
91C PHE* 3.5 22.2 - - + +
123C VAL* 4.1 21.0 - - + +
126C GLN 3.7 2.6 - - - +
127C PRO 3.2 14.1 - - - +
128C ASP* 1.3 86.7 - - - +
130C GLU* 1.3 63.7 + - - +
132C VAL* 3.3 5.2 + - + +
133C ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU* 5.7 2.7 + - - +
91C PHE* 2.9 39.3 - - + -
128C ASP* 3.3 3.6 + - - +
129C PRO* 1.3 78.6 - - - +
131C TRP* 1.3 63.2 + - - +
133C ALA* 3.3 3.3 + - - +
134C LEU* 3.0 22.8 + - + +
208C SER* 5.0 4.7 - - - -
211C ARG* 3.1 40.3 + - - +
215C TRP* 3.0 30.5 + - + +
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Residues in contact with TRP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ASP* 3.3 31.8 + - + +
130C GLU* 1.3 78.2 - - - +
132C VAL* 1.3 63.3 + - + +
134C LEU* 3.3 30.0 + - + +
135C VAL* 3.0 46.8 + - + +
189C PHE* 3.6 24.2 - + - -
201C SER* 2.9 23.9 + - - -
202C PHE* 3.7 18.1 - + - +
204C GLN 3.4 18.4 - - - -
205C PRO* 3.5 20.3 - - + +
206C VAL* 3.5 40.2 - - + -
211C ARG* 3.5 15.2 - - - +
214C LEU* 4.1 4.0 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C SER* 3.7 23.8 - - - +
122C GLY* 3.8 28.5 - - - +
123C VAL* 3.9 2.9 - - + +
126C GLN* 4.1 17.5 - - + -
128C ASP 3.3 14.5 + - - +
129C PRO* 3.3 8.0 + - + +
130C GLU 3.2 0.6 - - - -
131C TRP* 1.3 77.8 - - + +
133C ALA* 1.3 57.7 + - - +
135C VAL* 3.2 1.9 + - - +
136C MET* 2.8 44.0 + - + +
202C PHE* 3.9 31.9 - - + -
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 3.2 39.3 - - + -
95C MET* 3.0 28.4 - - + +
123C VAL* 4.6 2.2 - - + +
129C PRO 3.0 8.8 + - - +
130C GLU 3.5 1.8 - - - +
132C VAL* 1.3 76.8 - - - +
134C LEU* 1.3 57.6 + - - +
136C MET* 4.7 0.4 - - - -
137C SER* 2.8 36.4 + - - -
215C TRP* 4.2 7.1 - - + -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 3.0 10.9 + - + +
131C TRP* 3.6 38.1 - - + +
132C VAL 3.3 0.2 - - - -
133C ALA* 1.3 74.1 - - - +
135C VAL* 1.3 66.5 + - - +
137C SER* 3.8 1.6 - - - -
138C TYR* 3.3 45.8 + - + -
189C PHE* 4.5 2.7 - - + -
211C ARG* 4.1 20.9 - - + -
214C LEU* 4.0 30.7 - - + -
215C TRP* 3.6 48.2 - - + +
218C LEU* 5.2 0.4 - - + -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 3.0 55.7 + - + +
132C VAL 3.7 3.4 - - - +
134C LEU* 1.3 78.4 - - - +
136C MET* 1.3 58.8 + - - +
138C TYR* 3.4 2.3 + - - +
139C LYS* 2.9 32.4 + - + +
189C PHE* 4.2 10.3 - - + -
193C ALA* 5.6 4.0 - - + +
198C VAL* 4.4 15.9 - - + +
201C SER* 3.6 27.4 - - - +
202C PHE* 4.0 18.4 - - + -
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Residues in contact with MET 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MET* 4.3 5.6 - - - -
115C LEU* 3.4 35.4 - - + +
118C ALA* 3.5 15.7 - - + +
119C SER* 3.3 51.6 - - - +
132C VAL* 2.8 26.7 + - + +
133C ALA 4.3 2.0 - - - +
135C VAL* 1.3 74.3 - - - +
137C SER* 1.3 59.1 + - - +
139C LYS* 3.5 2.6 - - - +
140C LEU* 2.8 38.7 + - + +
198C VAL* 3.8 30.1 - - + -
202C PHE* 4.6 6.5 - - + -
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C LEU* 5.4 0.9 - - - +
95C MET* 3.5 16.7 - - - +
98C PHE* 3.3 41.3 - - - +
133C ALA 2.8 22.4 + - - -
134C LEU* 3.8 4.5 - - - -
135C VAL 3.3 0.2 - - - -
136C MET* 1.3 76.7 - - - +
138C TYR* 1.3 60.4 + - - +
140C LEU* 3.4 2.3 + - - -
141C LEU* 3.2 17.5 + - - +
215C TRP* 4.8 4.1 - - - -
218C LEU* 3.9 22.1 - - - +
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Residues in contact with TYR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LEU* 3.3 33.8 + - + +
135C VAL 3.9 2.9 - - - +
137C SER* 1.3 75.6 - - - +
139C LYS* 1.3 65.7 + - - +
141C LEU* 3.2 33.6 - - + +
142C GLY 3.8 0.2 + - - -
148C PRO* 5.0 9.6 - - + -
189C PHE* 3.6 33.0 - + + -
190C LEU* 3.6 25.4 - - + +
193C ALA* 4.7 7.9 - - + -
194C VAL* 3.4 28.3 - - + +
214C LEU 2.8 28.8 + - - -
217C ALA* 3.6 10.1 - - - +
218C LEU* 3.3 36.3 + - + -
221C PHE* 6.5 0.4 - - + -
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.6 23.2 - - + +
135C VAL* 2.9 22.0 + - + +
136C MET* 3.5 7.6 - - - +
137C SER 3.2 0.2 - - - -
138C TYR* 1.3 77.4 - - - +
140C LEU* 1.3 57.4 + - - +
142C GLY* 3.0 22.0 + - - -
143C LEU* 3.7 5.3 + - + +
193C ALA 3.7 11.6 + - - +
194C VAL* 2.9 31.8 + - - +
195C ARG 4.0 5.7 + - - -
196C ARG 3.4 28.0 + - - +
197C THR* 4.3 5.9 - - - +
198C VAL* 3.9 24.6 - - + +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MET* 5.0 8.5 - - - -
98C PHE* 4.2 19.7 - - + -
99C ALA* 4.5 16.8 - - + -
102C LEU* 3.7 10.7 - - + +
103C PHE* 4.1 20.1 - - + -
112C ALA 4.2 10.3 - - - +
115C LEU* 3.5 34.1 - - + -
116C PHE* 4.5 13.2 - - + +
119C SER* 5.9 0.4 - - - +
136C MET* 2.8 24.3 + - + +
137C SER 3.5 6.3 - - - +
139C LYS* 1.3 72.5 - - - +
141C LEU* 1.3 61.9 + - - +
143C LEU* 3.1 13.6 + - + +
144C ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.7 20.6 - - + -
102C LEU* 3.9 20.4 - - + -
137C SER 3.2 13.8 + - - +
138C TYR* 3.2 30.5 - - + +
139C LYS 3.2 0.4 - - - -
140C LEU* 1.3 77.8 - - - +
142C GLY* 1.3 57.0 + - - +
144C ALA* 3.5 2.9 + - - +
145C GLY 3.5 2.1 + - - -
146C VAL* 3.0 47.0 + - + +
147C ILE* 4.8 0.7 - - - -
148C PRO* 4.2 11.4 - - + -
194C VAL* 4.8 4.0 - - + -
218C LEU* 3.7 21.5 - - + -
221C PHE* 4.1 19.7 - - + -
222C VAL* 4.0 8.5 - - + -
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Residues in contact with GLY 142 (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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138C TYR 3.8 2.4 + - - -
139C LYS 3.0 10.5 + - - -
141C LEU* 1.3 74.8 - - - +
143C LEU* 1.3 58.0 + - - +
144C ALA 3.1 4.3 - - - -
145C GLY* 3.0 19.9 + - - -
147C ILE* 4.1 13.2 - - - +
194C VAL* 3.9 20.9 - - - +
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Residues in contact with LEU 143 (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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103C PHE* 3.5 16.8 - - + -
107C GLU* 5.9 0.7 - - - +
111C GLN* 3.9 34.3 - - + +
112C ALA* 3.8 26.9 - - + +
115C LEU* 3.3 36.6 - - + -
139C LYS* 3.7 5.4 + - + +
140C LEU* 3.1 11.6 + - + +
142C GLY* 1.3 75.0 - - - +
144C ALA* 1.3 57.3 + - - +
145C GLY 3.4 0.2 - - - -
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 3.9 19.5 - - + +
103C PHE* 3.7 21.3 - - + -
107C GLU* 4.1 15.5 - - - +
140C LEU 3.1 13.7 + - - +
141C LEU 3.9 2.9 - - - +
142C GLY 3.1 1.2 - - - -
143C LEU* 1.3 77.2 - - - +
145C GLY* 1.3 63.3 + - - +
146C VAL* 3.5 21.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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