Contacts of the helix formed by residues 19 - 34 (chain A) in PDB entry 1VLM
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 HIS 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TRP* 2.9 66.0 + + + +
16A PHE 3.9 3.8 - - - -
18A VAL* 1.3 99.3 - - + +
20A ARG* 1.3 57.6 + - - +
21A PHE 3.4 2.5 - - - -
22A ALA* 3.4 8.4 + - + -
23A TYR* 3.0 26.3 + - - +
180A HIS* 6.1 1.0 - - - -
181A PRO* 4.0 33.1 - - + +
182A SER* 4.1 13.3 + - - -
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Residues in contact with ARG 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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16A PHE 3.4 18.1 + - - +
17A LEU* 4.2 9.2 - - - +
18A VAL 3.6 3.0 + - - -
19A HIS* 1.3 76.4 - - - +
21A PHE* 1.3 70.9 + - + +
23A TYR* 3.2 17.9 + - - +
24A LEU* 2.9 66.4 + - + +
48A ARG* 5.8 1.2 - - - +
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Residues in contact with PHE 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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19A HIS 3.4 0.6 - - - -
20A ARG* 1.3 85.2 - - + +
22A ALA* 1.3 56.0 + - - +
24A LEU* 3.5 20.6 + - + +
25A SER* 2.7 35.7 + - - -
184A LEU* 3.3 31.2 - - + -
185A SER* 3.4 27.1 - - - -
186A GLU* 3.6 32.1 - - - +
187A ILE* 3.9 5.6 - - + -
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Residues in contact with ALA 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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15A TRP* 4.3 8.7 - - + -
19A HIS* 3.4 13.4 + - + +
20A ARG 3.3 0.2 - - - -
21A PHE* 1.3 75.7 - - - +
23A TYR* 1.3 63.2 + - - +
25A SER* 3.2 2.3 + - - -
26A GLU* 3.0 28.5 + - - +
177A LEU* 3.9 14.8 - - + +
181A PRO* 3.6 32.5 + - + +
184A LEU* 3.4 17.5 - - + +
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Residues in contact with TYR 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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15A TRP* 4.0 9.1 - - + -
16A PHE* 3.5 45.5 - + + +
19A HIS 3.0 14.3 + - - +
20A ARG* 3.4 23.3 - - - +
22A ALA* 1.3 75.9 - - - +
24A LEU* 1.3 65.0 + - + +
26A GLU* 3.3 5.1 + - - +
27A LEU* 3.0 45.3 + - + +
48A ARG* 2.3 67.6 + - - -
49A PHE* 4.3 9.4 - + - -
52A PRO* 3.8 10.6 - - - +
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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 ARG* 2.9 67.3 + - + +
21A PHE* 3.8 19.3 - - + +
22A ALA 3.3 0.2 - - - -
23A TYR* 1.3 75.0 - - + +
25A SER* 1.3 65.7 + - - +
27A LEU* 3.5 23.7 + - + +
28A GLN* 3.0 25.3 + - - +
187A ILE* 4.0 16.4 - - + +
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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 PHE 2.7 19.6 + - - -
22A ALA* 3.3 9.8 - - - -
24A LEU* 1.3 77.3 - - - +
26A GLU* 1.3 57.8 - - - +
28A GLN* 3.3 7.3 + - - +
29A ALA* 3.0 26.9 + - - +
176A THR* 3.7 22.5 + - - +
177A LEU* 3.9 13.5 - - - -
187A ILE* 3.8 6.9 - - - -
188A GLU* 2.8 33.1 + - - +
190A VAL* 5.1 0.5 - - - +
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Residues in contact with GLU 26 (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 TRP* 3.9 27.6 - - - -
16A PHE* 5.3 0.2 - - - -
22A ALA 3.0 17.2 + - - +
23A TYR* 3.6 7.1 - - - +
25A SER* 1.3 73.7 - - - +
27A LEU* 1.3 65.3 + - - +
29A ALA* 3.1 3.1 + - - +
30A VAL* 3.0 25.8 + - - +
49A PHE* 3.6 23.9 - - + -
97A VAL* 5.1 0.9 - - - +
98A THR* 5.7 2.6 - - - +
128A VAL* 5.1 4.5 - - - +
176A THR* 4.4 0.2 - - - -
177A LEU* 4.0 16.4 - - + +
199A PHE* 3.7 54.0 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.0 38.3 + - + +
24A LEU* 3.7 29.2 - - + +
25A SER 3.3 0.2 - - - -
26A GLU* 1.3 75.4 - - - +
28A GLN* 1.3 54.0 + - - +
30A VAL* 3.3 4.2 + - - +
31A LYS* 2.8 35.5 + - - +
48A ARG 3.9 2.7 - - - +
49A PHE* 3.4 31.6 - - + -
52A PRO* 3.7 33.9 - - + -
53A LEU* 4.2 16.1 - - + +
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Residues in contact with GLN 28 (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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24A LEU 3.0 15.3 + - - +
25A SER* 3.4 4.9 - - - +
27A LEU* 1.3 78.4 - - - +
29A ALA* 1.3 63.1 + - - +
31A LYS* 3.4 7.8 + - - +
32A CYS* 3.1 24.1 + - - -
187A ILE* 4.2 13.0 - - + +
188A GLU 3.1 24.6 - - - +
189A PRO* 4.1 2.8 - - - +
190A VAL* 3.5 23.4 + - + +
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Residues in contact with ALA 29 (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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25A SER 3.0 13.6 + - - +
26A GLU 3.1 8.0 + - - +
28A GLN* 1.3 75.2 - - - +
30A VAL* 1.3 64.1 + - - +
32A CYS* 3.4 17.5 - - - +
33A LEU 3.8 1.7 + - - -
174A VAL* 3.5 13.6 - - + +
175A GLN 5.1 2.0 - - - -
176A THR* 3.8 19.5 - - + -
190A VAL* 4.0 21.5 - - + -
199A PHE* 4.3 2.0 - - + +
201A VAL* 3.9 20.2 - - + +
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Residues in contact with VAL 30 (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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26A GLU 3.0 15.0 + - - +
27A LEU* 3.6 7.2 - - - +
29A ALA* 1.3 72.5 - - - +
31A LYS* 1.3 66.7 + - - +
33A LEU* 3.0 15.6 + - - +
34A LEU* 3.1 18.7 + - + +
49A PHE* 4.5 6.1 - - + -
53A LEU* 3.7 22.0 - - + -
95A LEU* 3.6 26.5 - - + -
97A VAL* 4.2 20.6 - - + -
124A ILE* 4.4 3.9 - - + +
126A GLY* 5.5 0.9 - - - -
199A PHE* 4.3 6.3 - - + -
201A VAL* 4.1 22.2 - - + -
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Residues in contact with LYS 31 (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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27A LEU 2.8 17.9 + - - +
28A GLN* 3.7 10.1 - - - +
30A VAL* 1.3 75.5 - - - +
32A CYS* 1.3 60.9 + - - +
33A LEU 3.3 0.7 + - - -
34A LEU* 3.4 23.0 + - + +
53A LEU* 4.1 18.8 - - + +
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Residues in contact with CYS 32 (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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28A GLN* 3.1 19.6 + - - -
29A ALA 3.4 11.0 - - - +
30A VAL 3.2 0.4 - - - -
31A LYS* 1.3 76.4 - - - +
33A LEU* 1.3 62.1 + - - +
34A LEU 5.1 0.9 - - - +
172A LYS* 5.8 0.7 + - - -
174A VAL* 4.4 15.9 - - + -
190A VAL* 4.0 26.9 - - - -
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Residues in contact with LEU 33 (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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29A ALA 3.8 0.9 + - - +
30A VAL 3.0 8.7 + - - +
32A CYS* 1.3 82.2 - - - +
34A LEU* 1.3 63.3 + - - +
35A PRO* 3.5 7.8 - - - +
124A ILE* 3.8 11.3 - - + +
172A LYS* 3.6 52.0 - - + +
174A VAL* 4.1 25.6 - - + -
201A VAL* 3.6 37.2 - - + +
203A ARG* 3.6 41.4 + - + +
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Residues in contact with LEU 34 (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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30A VAL* 3.1 24.1 + - + +
31A LYS* 3.4 16.2 + - + +
32A CYS 5.1 0.9 - - - +
33A LEU* 1.3 78.2 - - - +
35A PRO* 1.4 67.2 - - + +
53A LEU* 3.8 49.8 - - + +
55A ILE* 4.4 5.2 - - + -
93A PHE* 3.5 36.8 - - + -
95A LEU* 4.6 8.7 - - + -
124A ILE* 4.3 11.9 - - + -
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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
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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