Contacts of the helix formed by residues 131 - 147 (chain C) in PDB entry 1VLP
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 TYR 131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 4.1 21.5 - - + -
95C LEU* 3.5 23.3 - - + +
96C HIS 3.2 16.5 + - - -
97C PRO* 3.1 30.1 - - + +
100C GLN* 3.8 19.2 - - + +
101C ILE* 3.7 26.5 - - + -
121C VAL* 3.5 20.0 - - + -
127C ASP 3.5 19.3 - - - -
128C THR* 3.2 24.6 + - - +
130C LEU* 1.3 78.3 - - - +
132C GLU* 1.4 66.4 + - - +
133C ILE 3.2 0.3 + - - -
134C PRO* 3.4 5.2 - - + +
135C LEU* 2.9 39.2 + - + +
378C ILE* 6.3 0.2 - - + -
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Residues in contact with GLU 132 (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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15C TYR* 3.0 19.5 + - - -
16C LYS* 2.9 31.4 + - - +
34C TYR* 5.3 6.0 - - + -
128C THR 4.7 1.0 + - - -
129C ILE 4.1 1.2 + - - -
130C LEU 3.3 1.6 + - - -
131C TYR* 1.4 76.0 - - - +
133C ILE* 1.3 63.7 + - - +
135C LEU* 4.0 1.0 - - - +
136C LEU* 3.1 42.0 + - + +
180C ARG* 3.3 26.4 + - - -
233C GLU* 3.9 4.5 - - - +
378C ILE* 3.5 43.9 + - + +
379C LYS* 4.6 7.8 + - - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP 4.8 0.2 - - - +
12C THR* 3.3 22.4 - - - +
13C ASP* 3.0 31.2 - - - +
15C TYR* 3.9 4.3 - - - +
16C LYS* 3.5 27.8 - - + +
130C LEU 4.0 1.4 + - - -
132C GLU* 1.3 78.0 - - - +
134C PRO* 1.3 61.2 - - + +
136C LEU* 3.3 2.4 + - - +
137C SER* 2.9 27.7 + - - -
179C THR* 3.5 28.0 - - + -
180C ARG* 3.6 21.0 - - + +
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Residues in contact with PRO 134 (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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6C ILE* 4.1 28.9 - - + -
9C LEU* 6.4 2.0 - - + -
11C ASP 4.7 6.3 - - - +
12C THR* 4.0 11.0 - - - +
60C LEU* 4.4 14.4 - - + -
95C LEU* 6.1 4.0 - - + -
130C LEU* 3.1 23.6 - - + +
131C TYR* 3.4 8.3 - - - +
133C ILE* 1.3 94.3 - - + +
135C LEU* 1.4 54.6 + - - +
137C SER* 3.1 9.5 + - - +
138C LEU* 3.0 35.7 + - - +
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Residues in contact with LEU 135 (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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57C PHE* 3.6 32.3 - - + -
60C LEU* 3.7 19.7 - - + -
101C ILE* 4.0 14.1 - - + -
119C ILE* 4.6 8.1 - - + -
121C VAL* 3.8 22.2 - - + -
131C TYR* 2.9 46.3 + - + +
134C PRO* 1.4 72.9 - - - +
136C LEU* 1.3 57.3 + - - +
138C LEU* 3.3 3.5 + - - +
139C ILE* 2.9 39.3 + - + +
378C ILE* 3.6 20.9 - - + -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 4.8 3.1 - - + -
132C GLU* 3.1 35.0 + - + +
133C ILE 3.7 2.9 - - - +
135C LEU* 1.3 75.4 - - - +
137C SER* 1.3 59.2 + - - +
139C ILE* 3.2 1.0 + - + -
140C SER* 2.9 32.2 + - - -
180C ARG* 3.4 40.3 - - + +
181C ARG* 3.8 15.7 - - - +
376C ILE* 3.6 31.0 - - + +
377C VAL* 3.8 24.2 - - - +
378C ILE* 3.8 19.1 - - + +
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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
----------------------------------------------------------
5C VAL* 6.2 0.4 - - - -
6C ILE* 3.4 20.1 - - - +
11C ASP 5.5 0.3 + - - -
133C ILE 2.9 15.7 + - - -
134C PRO* 3.1 13.7 + - - +
136C LEU* 1.3 75.0 - - - +
138C LEU* 1.3 57.3 + - - +
140C SER* 3.7 3.1 + - - -
141C GLU* 3.0 30.4 + - - +
179C THR* 3.6 25.1 - - - +
180C ARG 3.5 7.2 + - - -
182C ARG* 3.5 24.5 + - - +
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Residues in contact with LEU 138 (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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5C VAL* 3.8 18.2 - - + -
6C ILE* 3.7 26.9 - - + -
52C TRP* 3.6 10.8 - - + -
53C LEU* 3.6 12.4 - - + +
56C GLN* 3.7 41.7 - - + +
57C PHE* 4.0 23.6 - - + -
60C LEU* 4.5 9.0 - - + -
134C PRO 3.0 23.9 + - - +
135C LEU* 3.6 3.6 - - - +
137C SER* 1.3 76.8 + - - +
139C ILE* 1.3 60.0 + - - +
141C GLU* 3.3 2.1 + - - -
142C ALA* 2.8 31.2 + - - +
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Residues in contact with ILE 139 (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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36C TYR* 3.9 25.6 - - + +
45C PHE* 3.5 27.1 - - + -
53C LEU* 3.8 20.9 - - + -
57C PHE* 4.1 9.0 - - + -
117C LEU* 4.3 3.1 - - + -
119C ILE* 3.7 27.4 - - + -
135C LEU* 2.9 29.7 + - + +
136C LEU* 4.6 3.1 - - - +
138C LEU* 1.3 76.5 - - - +
140C SER* 1.3 61.0 + - - +
142C ALA* 3.4 2.3 + - - +
143C TYR* 3.0 22.2 + - - +
374C LEU* 4.1 1.1 - - + -
376C ILE* 3.6 19.3 - - + -
378C ILE* 4.7 3.1 - - + -
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU 2.9 17.4 + - - -
137C SER 4.0 1.6 - - - -
139C ILE* 1.3 75.2 - - - +
141C GLU* 1.3 63.9 + - - +
143C TYR* 3.2 2.8 + - - +
144C PHE* 3.2 33.9 + - - -
180C ARG 4.3 9.0 - - - -
181C ARG* 3.6 13.6 + - - +
182C ARG 2.6 26.3 + - - -
183C ARG 4.3 0.4 - - - -
359C ASN* 3.8 8.7 + - - -
374C LEU* 4.2 13.3 + - - +
376C ILE* 3.9 7.7 - - - +
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Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.5 34.7 - - + +
52C TRP* 4.1 12.5 - - + -
137C SER 3.0 19.3 + - - +
138C LEU* 3.3 5.8 + - - +
140C SER* 1.3 75.9 - - - +
142C ALA* 1.3 57.2 + - - +
144C PHE* 3.2 3.8 + - - +
145C LYS* 2.9 43.2 + - + +
182C ARG* 4.3 2.6 + - - -
183C ARG 3.5 13.3 + - - +
184C SER* 3.8 19.7 - - - -
185C LEU* 2.9 26.3 + - - +
186C LYS 5.6 0.2 + - - -
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Residues in contact with ALA 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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45C PHE* 4.8 0.4 - - + -
49C ALA* 4.2 10.6 - - + +
52C TRP* 3.5 27.5 - - + -
53C LEU* 3.7 20.9 - - + -
138C LEU 2.8 17.1 + - - +
139C ILE 3.6 4.5 - - - +
141C GLU* 1.3 77.1 - - - +
143C TYR* 1.3 62.1 + - - +
145C LYS* 4.3 0.4 - - - -
146C PHE* 3.0 35.7 + - + +
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Residues in contact with TYR 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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43C LEU* 3.6 39.6 - - + +
44C THR 3.4 31.3 + - - -
45C PHE* 3.9 20.8 - + + -
139C ILE 3.0 14.6 + - - +
140C SER 3.2 8.0 + - - +
142C ALA* 1.3 76.6 - - - +
144C PHE* 1.3 85.1 + + + +
145C LYS 3.3 0.2 - - - -
147C VAL* 2.9 50.8 + - + +
148C ASP* 2.9 34.2 + - + +
372C GLU 5.3 0.7 - - - -
374C LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 144 (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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140C SER* 3.2 32.5 + - - +
141C GLU 3.6 0.4 - - - -
143C TYR* 1.3 100.7 - + - +
145C LYS* 1.3 60.3 + - - +
148C ASP* 3.1 28.3 - - + +
149C ILE* 4.1 3.5 - - - +
151C TRP* 3.0 32.1 + - + +
183C ARG* 3.4 66.6 - - + +
359C ASN* 3.6 17.9 - - - -
371C SER* 4.2 0.4 - - - -
372C GLU 3.4 23.1 - - - -
373C PRO* 3.9 4.5 - - + -
374C LEU* 4.0 11.0 - - + -
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Residues in contact with LYS 145 (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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5C VAL* 6.3 0.6 - - - +
52C TRP* 4.0 27.6 - - + +
141C GLU* 2.9 28.5 + - + +
143C TYR 3.3 0.2 - - - -
144C PHE* 1.3 81.5 - - - +
146C PHE* 1.3 96.3 + - + +
149C ILE* 3.3 15.5 - - - +
151C TRP* 5.4 0.9 - - - -
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASN* 3.0 31.4 + - - +
48C GLU* 3.9 21.2 - - + +
49C ALA* 3.9 16.6 - - + -
52C TRP* 3.4 46.9 - + + -
142C ALA* 3.0 18.7 + - - +
145C LYS* 1.3 114.5 - - + +
147C VAL* 1.3 63.1 + - - +
149C ILE* 4.3 5.9 - - - +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 3.4 27.1 - - - +
45C PHE* 4.1 3.8 - - + -
46C ASN* 3.9 30.3 - - + +
49C ALA* 4.2 9.9 - - + -
114C HIS* 5.8 6.3 - - + +
143C TYR* 2.9 39.6 + - + +
146C PHE* 1.3 83.2 - - - +
148C ASP* 1.3 61.9 + - - +
149C ILE* 3.7 5.7 + - - +
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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
------------------------------------------------------------
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