Contacts of the helix formed by residues 126 - 136 (chain F) in PDB entry 1VLH
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 SER 126 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 3.3 17.7 + - - +
13F THR* 4.2 8.1 - - - -
16F HIS* 6.0 0.2 - - - -
89F ARG* 3.7 24.0 - - - +
91F VAL* 5.2 1.1 - - - -
125F ILE* 1.3 77.9 - - - +
127F SER* 1.3 61.9 + - - +
128F SER* 3.4 12.4 + - - -
129F LEU* 3.0 20.6 + - - +
130F VAL* 3.2 24.6 + - - +
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F SER* 6.5 0.2 - - - -
9F PHE 5.3 0.2 + - - -
10F ASP* 3.5 24.8 + - - -
11F PRO* 2.5 25.4 + - - -
13F THR* 3.8 10.2 - - - +
16F HIS* 3.4 17.3 - - - -
40F LYS* 6.4 0.4 - - - -
89F ARG* 4.9 1.4 - - - +
126F SER* 1.3 72.6 - - - +
128F SER* 1.3 59.6 + - - +
130F VAL* 3.3 4.8 + - - +
131F LYS* 2.9 37.7 + - - +
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Residues in contact with SER 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.0 31.7 + - - +
40F LYS* 6.5 1.6 - - - -
126F SER* 3.2 10.1 + - - -
127F SER* 1.3 80.8 - - - +
129F LEU* 1.3 59.2 + - - +
131F LYS* 3.9 16.4 - - - +
132F GLU* 3.1 24.9 + - - +
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Residues in contact with LEU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.1 7.6 - - - +
99B GLN* 3.7 19.1 - - + +
100B MET* 5.5 1.1 - - + -
103B ALA* 3.7 33.7 - - + -
200B PNS 3.9 17.7 - - - -
124F PHE 4.1 18.6 - - - +
125F ILE* 4.3 12.3 - - + -
126F SER* 3.0 21.2 + - - +
128F SER* 1.3 76.0 + - - +
130F VAL* 1.3 59.2 + - - +
132F GLU* 3.3 7.9 + - - +
133F VAL* 2.9 33.1 + - + +
143F TRP* 4.0 22.0 - - + -
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Residues in contact with VAL 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PRO* 4.4 7.6 - - + -
13F THR* 4.1 10.1 - - + -
125F ILE* 5.1 2.2 - - + -
126F SER 3.2 12.9 + - - +
127F SER* 3.3 10.1 + - - +
129F LEU* 1.3 80.3 - - + +
131F LYS* 1.3 57.9 + - - +
133F VAL 3.4 0.3 + - - -
134F ALA* 2.8 32.4 + - - +
140F VAL* 3.5 13.4 - - + +
143F TRP* 4.0 27.4 - - + -
144F VAL* 3.6 28.0 - - + -
152F LEU* 3.4 29.4 - - + -
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Residues in contact with LYS 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASP* 2.9 41.5 + - - +
11F PRO* 3.8 13.7 - - + -
40F LYS* 6.1 3.6 - - - +
41F LYS 5.0 5.9 + - - -
43F MET* 3.8 42.7 - - + +
127F SER* 2.9 20.2 + - - +
128F SER* 3.9 15.7 - - - +
130F VAL* 1.3 78.4 - - - +
132F GLU* 1.3 58.3 + - - +
134F ALA* 3.8 4.4 - - - +
135F LEU* 2.8 41.9 + - + +
152F LEU* 4.2 4.0 - - + -
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASN* 5.0 0.7 - - - +
38B PRO* 3.4 37.0 - - + +
39B ARG* 2.6 40.1 + - - +
96B TYR* 5.5 4.1 + - - -
100B MET* 5.6 1.6 - - - +
200B PNS 3.0 44.4 + - - +
128F SER 3.1 14.2 + - - +
129F LEU* 3.3 8.6 + - - +
131F LYS* 1.3 81.5 - - - +
133F VAL* 1.3 59.5 + - - +
135F LEU* 3.6 5.7 + - - +
136F TYR* 3.0 32.5 + - + -
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.3 7.9 - - + +
107B LEU* 3.9 29.2 - - + -
200B PNS 4.3 12.1 - - - -
129F LEU* 2.9 35.9 + - + +
132F GLU* 1.3 73.8 - - - +
134F ALA* 1.3 64.5 + - - +
136F TYR* 3.1 10.4 + - - +
137F GLY 3.2 0.2 + - - -
138F GLY* 2.9 39.5 + - - -
140F VAL* 3.6 22.4 - - + -
143F TRP* 3.8 18.2 - - + -
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F VAL 2.8 22.0 + - - +
131F LYS* 3.8 4.0 - - - +
133F VAL* 1.3 71.9 - - - +
135F LEU* 1.3 55.2 + - - +
137F GLY* 2.6 26.7 + - - -
138F GLY 3.9 11.4 - - - -
140F VAL* 3.7 10.3 - - + +
152F LEU* 4.1 21.3 - - + -
156F LEU* 3.2 24.9 - - + +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F MET* 3.6 20.6 - - + -
131F LYS* 2.8 30.2 + - + +
132F GLU* 3.9 7.6 - - - +
133F VAL 3.2 0.2 - - - -
134F ALA* 1.3 73.7 - - - +
136F TYR* 1.3 65.0 + - + +
137F GLY 3.3 0.4 + - - -
156F LEU* 3.2 38.7 - - + +
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Residues in contact with TYR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 2.7 23.2 + - - -
38B PRO* 3.4 39.7 - - + +
69B HIS 3.3 20.9 - - - -
70B GLY* 3.4 24.2 - - - -
71B LEU* 3.7 32.4 + - + +
74B ASP* 4.5 5.4 - - - +
200B PNS 3.6 24.9 - - + -
132F GLU* 3.0 25.6 - - + -
133F VAL 3.1 7.1 + - - +
135F LEU* 1.3 83.6 - - + +
137F GLY* 1.3 60.1 + - - +
138F GLY 3.4 2.4 + - - -
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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