Contacts of the helix formed by residues 131 - 147 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 6.4 0.2 - - + -
60A LEU* 4.1 20.6 - - + -
95A LEU* 3.7 22.7 - - + +
96A HIS 3.3 17.0 + - - -
97A PRO* 3.1 29.8 - - + +
100A GLN* 3.7 17.7 - - + +
101A ILE* 3.7 27.6 - - + -
121A VAL* 3.5 19.5 - - + -
127A ASP 3.4 20.9 - - - -
128A THR* 3.1 24.8 + - - +
130A LEU* 1.3 77.0 - - - +
132A GLU* 1.3 67.5 + - - +
133A ILE 3.2 0.7 + - - -
134A PRO* 3.3 5.1 - - + +
135A LEU* 3.0 37.9 + - + +
378A ILE* 6.2 0.2 - - + -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 2.8 29.7 + - - -
16A LYS* 3.0 29.5 + - - +
34A TYR* 5.3 7.6 - - + -
128A THR 4.6 1.2 + - - -
129A ILE 4.1 1.2 + - - -
130A LEU 3.4 1.4 + - - -
131A TYR* 1.3 77.4 - - - +
133A ILE* 1.3 66.9 + - - +
135A LEU* 3.8 1.2 - - - +
136A LEU* 3.0 40.6 + - + +
180A ARG* 3.4 17.0 + - - -
233A GLU* 4.0 2.9 - - - +
378A ILE* 3.6 42.9 + - + +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 4.8 0.4 - - - +
12A THR* 3.2 26.0 - - - +
13A ASP* 2.9 30.3 - - - +
15A TYR* 3.4 15.5 - - - +
16A LYS* 3.4 18.2 - - + -
130A LEU 4.0 0.8 + - - -
132A GLU* 1.3 78.5 - - - +
134A PRO* 1.3 68.0 - - + +
136A LEU* 3.7 1.6 - - - +
137A SER* 2.8 31.4 + - - +
179A THR* 3.3 33.4 - - + -
180A ARG* 3.1 30.0 - - + -
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.2 31.0 - - + -
11A ASP 4.7 5.6 - - - +
12A THR* 4.1 9.0 - - - +
60A LEU* 4.3 16.6 - - + -
95A LEU* 6.0 4.0 - - + -
130A LEU* 3.1 22.4 - - + +
131A TYR* 3.3 9.0 - - + +
133A ILE* 1.3 96.6 - - + +
135A LEU* 1.3 55.0 + - - +
137A SER* 3.7 7.1 - - - +
138A LEU* 2.8 35.6 + - - +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.5 33.4 - - + -
60A LEU* 3.8 19.5 - - + -
101A ILE* 4.0 12.1 - - + -
119A ILE* 4.5 9.6 - - + -
121A VAL* 3.8 21.5 - - + -
131A TYR* 3.0 42.3 + - + +
134A PRO* 1.3 76.8 - - - +
136A LEU* 1.3 58.5 + - - +
138A LEU* 3.3 3.4 + - + +
139A ILE* 2.9 39.9 + - + +
378A ILE* 3.6 20.9 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 4.9 3.1 - - + -
132A GLU* 3.0 34.9 + - + +
133A ILE 3.7 2.7 - - - +
135A LEU* 1.3 75.0 - - - +
137A SER* 1.3 57.7 + - - +
139A ILE* 3.3 1.1 + - + -
140A SER* 3.0 31.9 + - - -
180A ARG* 3.6 42.9 - - + +
181A ARG* 6.1 0.9 - - + -
376A ILE* 3.6 45.0 - - + +
377A VAL* 3.9 19.1 - - - -
378A ILE* 3.9 20.2 - - + +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 6.3 0.4 - - - -
6A ILE* 4.5 2.5 - - - -
11A ASP 5.7 0.2 + - - -
133A ILE* 2.8 22.8 + - - +
134A PRO* 3.7 8.0 - - - +
136A LEU* 1.3 72.1 - - - +
138A LEU* 1.3 57.9 + - - +
140A SER* 3.9 3.5 - - - -
141A GLU* 3.0 30.5 + - - +
179A THR* 3.0 34.8 + - - +
180A ARG 3.6 6.5 + - - -
182A ARG* 3.7 33.3 + - - +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.9 16.4 - - + -
6A ILE* 3.8 26.7 - - + -
52A TRP* 3.6 12.9 - - + -
53A LEU* 3.6 13.1 - - + +
56A GLN* 3.7 43.5 - - + +
57A PHE* 3.9 23.8 - - + -
60A LEU* 4.4 9.0 - - + -
134A PRO 2.8 23.4 + - - +
135A LEU 3.6 4.0 - - - +
137A SER* 1.3 75.2 - - - +
139A ILE* 1.3 59.5 + - - +
141A GLU* 3.3 2.7 + - + -
142A ALA* 2.8 31.0 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.8 21.1 - - + +
45A PHE* 3.7 25.0 - - + -
53A LEU* 3.9 12.3 - - + -
57A PHE* 4.1 16.6 - - + -
117A LEU* 4.1 7.4 - - + -
119A ILE* 3.7 26.5 - - + -
135A LEU* 2.9 27.1 + - + +
136A LEU* 3.3 4.5 + - + +
138A LEU* 1.3 71.4 - - - +
140A SER* 1.3 65.7 + - - +
142A ALA* 3.3 3.6 + - - +
143A TYR* 3.0 23.0 + - - +
374A LEU* 4.0 1.3 - - + -
376A ILE* 3.6 21.1 - - + -
378A ILE* 4.6 5.8 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU 3.0 16.6 + - - -
137A SER 3.9 1.8 - - - -
139A ILE* 1.3 76.1 - - - +
141A GLU* 1.3 63.6 + - - +
143A TYR* 3.2 3.0 + - - +
144A PHE* 3.1 33.1 + - - -
180A ARG 4.6 6.3 - - - -
181A ARG* 3.9 4.9 + - - +
182A ARG 2.7 27.5 + - - -
183A ARG* 4.0 2.5 - - - -
359A ASN* 3.8 13.0 + - - -
374A LEU* 4.3 15.6 + - - +
376A ILE* 4.1 6.6 - - - +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.4 34.7 - - + +
52A TRP* 4.1 12.2 - - + -
137A SER 3.0 19.5 + - - +
138A LEU* 3.7 5.8 - - - +
140A SER* 1.3 77.4 - - - +
142A ALA* 1.3 56.8 + - - +
144A PHE* 3.3 1.2 + - - +
145A LYS* 2.9 45.9 + - + +
182A ARG* 4.4 1.6 + - - -
183A ARG 3.4 12.0 + - - +
184A SER* 3.3 19.5 - - - -
185A LEU* 3.0 24.8 + - - +
186A LYS 5.6 0.3 + - - -
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.7 0.9 - - + -
49A ALA* 4.3 12.1 - - + +
52A TRP* 3.7 17.6 - - + -
53A LEU* 3.7 29.8 - - + -
138A LEU 2.8 21.3 + - - +
139A ILE 3.5 5.6 - - - +
141A GLU* 1.3 71.1 - - - +
143A TYR* 1.3 65.4 + - - +
145A LYS* 4.3 0.4 - - - -
146A PHE* 2.9 34.5 + - + +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.5 42.2 - - + +
44A THR 3.2 31.9 + - - -
45A PHE* 3.9 19.9 - + + -
139A ILE 3.0 14.1 + - - +
140A SER 3.2 8.3 + - - +
142A ALA* 1.3 75.3 - - - +
144A PHE* 1.3 85.2 + + + +
147A VAL* 2.8 52.6 + - + +
148A ASP* 3.0 33.1 + - + +
372A GLU 5.3 0.7 - - - -
374A LEU* 3.8 19.5 - - + -
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER* 3.1 32.4 + - - +
141A GLU 3.7 0.7 - - - +
143A TYR* 1.3 93.2 - + - +
145A LYS* 1.3 60.3 + - - +
148A ASP* 3.1 38.8 - - + +
149A ILE* 4.2 3.5 - - - +
151A TRP* 2.9 37.5 + + + +
183A ARG* 3.4 61.5 - - + +
359A ASN* 3.9 17.5 - - - -
372A GLU 3.3 23.1 - - - -
373A PRO* 3.9 3.8 - - + -
374A LEU* 4.1 11.7 - - + -
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 6.1 0.2 - - - -
52A TRP* 4.1 26.7 - - + +
141A GLU* 2.9 29.5 + - + +
142A ALA 3.7 2.9 - - - +
144A PHE* 1.3 79.8 - - - +
146A PHE* 1.3 94.2 + - + +
149A ILE* 3.5 16.1 - - - +
151A TRP* 5.3 0.9 - - - -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 3.1 29.4 + - - +
48A GLU* 3.3 41.8 - - + +
49A ALA* 3.8 19.7 - - + +
52A TRP* 3.4 48.7 - + + -
142A ALA* 2.9 24.4 + - - +
145A LYS* 1.3 110.9 - - + +
147A VAL* 1.3 63.8 + - - +
149A ILE* 4.6 5.8 - - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.2 28.9 - - - +
45A PHE* 4.1 3.8 - - + -
46A ASN* 3.9 30.1 - - - +
49A ALA* 4.2 8.1 - - + -
143A TYR* 2.8 48.5 + - + +
146A PHE* 1.3 76.9 - - - +
148A ASP* 1.3 59.1 + - + +
149A ILE* 3.8 5.7 + - - +
387B HIS* 4.7 14.0 + - + +
401B ASP* 5.1 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
------------------------------------------------------------
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