Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 2VL7
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 GLN 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ARG* 1.3 79.2 - - - +
11A TRP* 1.3 64.3 + - - +
12A GLN 3.3 0.4 + - - -
13A ALA* 3.6 6.1 + - - +
14A GLU* 3.3 29.6 + - - +
345A GLU* 3.4 27.8 + - - +
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Residues in contact with TRP 11 (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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9A ARG 3.5 17.5 - - - +
10A GLN* 1.3 79.8 - - - +
12A GLN* 1.3 81.8 + - + +
14A GLU* 3.6 20.0 - - - +
15A LYS* 2.9 33.2 + - + +
31A LEU* 4.4 9.2 - - + -
33A ALA* 4.5 5.8 - - + -
37A LEU* 3.0 48.0 + - + +
38A GLY 3.8 6.3 - - - -
39A LYS* 4.3 7.9 - - - -
42A PHE* 3.5 44.0 - + + -
343A VAL* 3.1 50.7 - - + -
345A GLU* 3.4 23.3 + - + +
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Residues in contact with GLN 12 (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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9A ARG* 3.6 36.5 - - + +
11A TRP* 1.3 98.2 - - + +
13A ALA* 1.3 62.2 + - + +
16A LEU* 3.5 10.9 + - - +
37A LEU 3.8 4.4 + - - -
38A GLY* 2.8 31.3 + - - -
41A VAL* 3.9 14.5 - - - +
42A PHE* 3.0 61.2 + - - +
45A VAL* 4.8 5.9 - - - +
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Residues in contact with ALA 13 (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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9A ARG 4.9 4.9 + - - +
10A GLN* 3.6 7.7 + - - +
11A TRP 3.2 0.6 - - - -
12A GLN* 1.3 78.8 - - + +
14A GLU* 1.3 64.5 + - - +
16A LEU* 3.8 15.7 + - - +
17A GLY 4.8 1.2 + - - -
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Residues in contact with GLU 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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10A GLN* 3.3 13.6 + - - +
11A TRP* 3.6 28.1 - - - +
13A ALA* 1.3 79.6 - - - +
15A LYS* 1.3 84.6 + - + +
16A LEU 3.7 0.2 + - - -
17A GLY 4.6 3.5 + - - -
18A GLU* 5.0 3.5 + - - +
345A GLU* 5.3 0.7 - - - +
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Residues in contact with LYS 15 (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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11A TRP* 2.9 24.2 + - + +
14A GLU* 1.3 99.2 - - + +
16A LEU* 1.3 63.7 + - - +
17A GLY 3.5 0.4 - - - -
18A GLU* 3.3 33.1 + - - +
19A ALA* 3.1 22.7 + - - +
42A PHE* 4.1 10.3 - - + -
341A ILE* 3.9 29.6 - - + +
342A VAL 4.1 17.3 + - - +
343A VAL* 4.5 12.6 - - + +
344A ASN 6.1 0.2 - - - +
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Residues in contact with LEU 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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12A GLN 3.5 15.0 + - - +
13A ALA* 3.9 12.1 - - - +
14A GLU 3.4 1.2 - - - -
15A LYS* 1.3 76.7 - - - +
17A GLY* 1.3 60.4 + - - +
19A ALA* 3.2 2.8 + - - +
20A ILE* 2.8 40.0 + - + +
42A PHE* 3.9 19.5 - - + -
45A VAL* 3.9 31.2 - - + -
46A LEU* 3.9 27.1 - - + +
49A GLN* 4.8 17.3 - - + +
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Residues in contact with GLY 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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13A ALA 4.8 1.6 + - - -
14A GLU 4.6 3.2 + - - -
15A LYS 3.5 0.6 - - - -
16A LEU* 1.3 78.1 - - - +
18A GLU* 1.3 56.8 + - - +
20A ILE* 3.9 6.3 - - - +
21A ASN* 3.0 40.2 + - - +
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Residues in contact with GLU 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 GLU 5.0 2.7 + - - +
15A LYS* 3.3 45.2 + - + +
16A LEU 3.2 0.4 - - - -
17A GLY* 1.3 77.3 - - - +
19A ALA* 1.3 56.0 + - - +
21A ASN* 3.8 3.3 - - - +
22A ALA* 2.9 30.5 + - - +
339A TYR* 2.6 38.4 + - + +
340A LYS 4.7 1.9 - - - +
341A ILE* 3.7 18.5 - - + +
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Residues in contact with ALA 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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15A LYS 3.1 13.9 + - - +
16A LEU 3.6 6.7 - - - +
18A GLU* 1.3 74.0 - - - +
20A ILE* 1.3 64.2 + - - +
22A ALA* 3.3 2.4 + - - +
23A LEU* 3.0 31.4 + - - +
29A LEU* 3.7 27.6 - - + -
42A PHE* 3.8 16.2 - - + -
46A LEU* 4.0 8.5 - - + -
341A ILE* 3.6 12.3 - - + +
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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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16A LEU* 2.8 29.7 + - + +
17A GLY* 3.9 6.7 - - - +
19A ALA* 1.3 70.8 - - - +
21A ASN* 1.3 61.9 + - - +
23A LEU* 3.2 4.7 + - - +
24A LYS* 2.8 57.1 + - + +
46A LEU* 3.2 28.0 - - + +
49A GLN* 4.0 31.6 - - + +
50A LEU* 3.7 26.2 - - + +
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Residues in contact with ASN 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 GLY* 3.0 23.9 + - - +
18A GLU* 3.9 4.2 - - - +
20A ILE* 1.3 76.2 - - - +
22A ALA* 1.3 67.3 + - - +
24A LYS* 4.4 12.9 - - - +
25A HIS* 2.9 46.0 + - + +
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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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18A GLU 2.9 18.0 + - - +
19A ALA 3.5 5.4 - - - +
21A ASN* 1.3 79.0 - - - +
23A LEU* 1.3 60.6 + - + +
25A HIS* 3.2 7.6 + - - -
26A GLY 3.3 0.2 + - - -
27A LYS* 3.0 32.4 + - + +
29A LEU* 4.1 12.8 - - + -
339A TYR* 3.9 36.8 - - + -
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Residues in contact with LEU 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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19A ALA 3.0 21.7 + - - +
20A ILE 3.7 2.2 - - - +
22A ALA* 1.3 73.5 - - - +
24A LYS* 1.3 67.2 + - - +
26A GLY* 3.1 14.7 + - - -
27A LYS 3.5 16.3 - - - +
29A LEU* 3.9 14.6 - - + -
46A LEU* 3.9 26.5 - - + -
50A LEU* 3.6 26.0 - - + -
178A LEU* 4.3 3.6 - - + -
321A PHE* 3.4 29.5 - - + -
322A LYS 3.4 37.0 - - - +
323A VAL* 4.1 7.2 - - + -
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Residues in contact with LYS 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* 2.8 42.4 + - + +
21A ASN* 4.0 14.4 - - - +
23A LEU* 1.3 73.1 - - - +
25A HIS* 1.3 65.1 + - + +
26A GLY 3.2 2.9 + - - -
49A GLN 6.1 0.4 - - - -
50A LEU* 4.3 16.4 - - + -
321A PHE* 4.2 10.5 - - + -
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Residues in contact with HIS 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 ASN* 2.9 43.2 + - + +
22A ALA* 3.2 4.0 + - - +
23A LEU 3.1 0.8 - - - -
24A LYS* 1.3 82.0 - - + +
26A GLY* 1.3 59.9 + - - +
27A LYS* 3.4 14.1 + - + +
337A ASN* 5.2 0.7 + - - -
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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
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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