Contacts of the helix formed by residues 13 - 25 (chain A) 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 THR 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PRO* 3.5 15.0 - - + +
12A ILE* 1.3 75.2 - - - +
14A LEU* 1.3 64.3 + - - +
15A GLY* 3.4 9.9 + - - -
16A HIS* 2.9 30.1 + - + +
17A VAL* 3.1 14.9 + - - +
125A ILE* 3.8 11.6 - - - +
126A SER* 4.3 3.1 - - - -
127A SER* 3.6 26.0 - - - +
130A VAL* 4.1 16.4 - - + -
143A TRP 3.3 12.6 - - - +
144A VAL* 4.3 4.0 - - + -
145A PRO* 4.1 8.1 - - - -
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Residues in contact with LEU 14 (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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13A THR* 1.3 70.5 - - - +
15A GLY* 1.3 56.8 + - - +
17A VAL* 3.3 13.8 + - + +
18A ASP* 2.9 29.5 + - - +
122A PHE* 3.5 27.7 - - + -
141A THR 4.5 2.5 - - - +
142A GLU* 3.6 24.5 - - - +
143A TRP 2.8 20.4 + - - +
144A VAL 3.7 12.3 - - - +
145A PRO* 3.8 25.7 - - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.1 7.7 + - - -
14A LEU* 1.3 77.4 - - - +
16A HIS* 1.3 61.7 + - - +
18A ASP* 3.3 5.2 + - - +
19A ILE* 3.2 27.4 + - - +
118A ALA* 6.0 1.8 - - - +
122A PHE* 3.6 35.0 - - - -
125A ILE* 4.2 3.3 - - - +
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Residues in contact with HIS 16 (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 TYR* 3.4 23.4 - - + +
9A PHE* 4.0 26.0 + + + -
11A PRO 3.7 3.6 - - - -
12A ILE* 3.4 19.3 - - + -
13A THR* 2.9 33.6 + - + +
15A GLY* 1.3 73.3 - - - +
17A VAL* 1.3 60.1 + - - +
19A ILE* 3.2 3.5 + - - +
20A ILE* 2.9 33.4 + - - +
89A ARG* 4.7 15.6 + - - -
126A SER* 6.0 0.2 - - - -
127A SER* 3.3 28.2 + - - -
200A PNS 5.8 1.6 + - - -
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Residues in contact with VAL 17 (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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12A ILE* 3.9 10.3 - - + -
13A THR 3.1 14.3 + - - +
14A LEU* 3.3 16.1 + - + +
16A HIS* 1.3 76.4 - - - +
18A ASP* 1.3 57.5 + - - +
20A ILE* 3.3 10.7 + - - +
21A LYS* 2.9 48.4 + - + +
56A VAL* 3.7 29.2 - - + -
57A LEU* 4.8 10.1 - - + -
145A PRO* 4.2 10.5 - - + -
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Residues in contact with ASP 18 (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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14A LEU 2.9 13.4 + - - +
15A GLY 3.4 10.5 - - - +
17A VAL* 1.3 76.9 - - - +
19A ILE* 1.3 58.7 + - - +
21A LYS* 3.4 14.1 + - - +
22A ARG* 3.0 62.5 + - - -
118A ALA* 5.3 0.7 - - - -
119A SER* 4.1 22.7 + - - -
122A PHE* 4.2 18.4 - - + -
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Residues in contact with ILE 19 (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 TYR* 3.7 33.9 - - + +
15A GLY 3.2 14.8 + - - +
16A HIS 3.2 6.0 + - - +
18A ASP* 1.3 75.5 - - - +
20A ILE* 1.3 61.3 + - - +
22A ARG* 3.7 9.5 - - - +
23A ALA* 2.7 29.7 + - + +
85A VAL* 4.3 12.6 - - + -
87A GLY* 4.2 19.3 - - - +
116A LEU* 4.0 36.1 - - + +
117A ILE 4.4 11.7 - - - +
118A ALA* 4.5 11.7 - - + -
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Residues in contact with ILE 20 (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 TYR* 3.4 24.2 - - + -
9A PHE* 5.2 0.2 - - + -
12A ILE* 4.0 25.6 - - + -
16A HIS* 2.9 21.8 + - + +
17A VAL* 3.4 7.0 - - - +
19A ILE* 1.3 77.2 - - - +
21A LYS* 1.3 63.0 + - - +
23A ALA* 3.6 2.5 - - - +
24A LEU* 3.1 24.1 + - - +
30A LEU* 3.8 17.6 - - + +
32A VAL* 3.8 23.1 - - + -
57A LEU* 4.1 14.8 - - + -
60A LEU* 3.8 23.3 - - + -
63A VAL* 4.1 9.2 - - + -
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Residues in contact with LYS 21 (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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17A VAL* 2.9 40.9 + - + +
18A ASP* 3.7 13.5 - - - +
20A ILE* 1.3 73.1 - - - +
22A ARG* 1.3 64.9 + - + +
24A LEU* 3.3 17.6 + - - +
25A SER* 3.5 9.4 + - - -
60A LEU* 4.0 28.3 - - + +
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Residues in contact with ARG 22 (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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18A ASP* 3.0 50.3 + - - +
19A ILE* 3.9 9.3 - - - +
21A LYS* 1.3 76.1 - - + +
23A ALA* 1.3 63.2 + - - +
25A SER* 2.3 31.6 + - - +
26A ILE* 3.9 6.2 + - - +
116A LEU* 3.9 17.2 - - + +
117A ILE* 2.7 33.4 + - - +
119A SER* 5.5 2.5 - - - -
105B LYS* 3.1 34.8 - - - +
112B GLU* 2.7 53.4 + - - +
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Residues in contact with ALA 23 (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 TYR* 6.2 0.7 - - + -
19A ILE* 2.7 24.2 + - + +
20A ILE 3.6 4.5 - - - +
22A ARG* 1.3 73.1 - - - +
24A LEU* 1.3 57.5 + - - +
26A ILE* 3.0 7.5 + - - +
27A PHE* 2.9 39.4 + - + -
30A LEU* 4.3 22.4 - - + -
85A VAL* 4.4 14.1 - - + -
116A LEU* 3.9 14.0 - - + +
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Residues in contact with LEU 24 (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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20A ILE 3.1 17.3 + - - +
21A LYS* 3.5 9.9 - - - +
22A ARG 3.2 0.4 - - - -
23A ALA* 1.3 77.2 - - - +
25A SER* 1.3 58.6 + - - +
26A ILE 3.1 0.7 - - - -
27A PHE 3.2 26.0 - - - +
28A ASP* 4.1 9.2 - - - +
30A LEU* 3.9 16.2 - - + -
60A LEU* 3.5 26.2 - - + -
61A ASP 3.8 8.5 - - - +
62A GLY* 3.7 27.8 - - - +
63A VAL* 3.2 26.0 - - + -
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Residues in contact with SER 25 (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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21A LYS 3.5 5.9 + - - -
22A ARG* 2.3 30.1 + - - +
24A LEU* 1.3 77.0 - - - +
26A ILE* 1.3 63.6 + - - +
1B MET* 4.0 12.0 - - - +
110B ASP 5.7 2.4 + - - -
112B GLU* 4.4 10.6 + - - +
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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