Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 2VUU
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 GLY 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ASN* 2.7 22.5 + - - -
14A THR* 1.3 72.3 - - - +
16A ARG* 1.3 59.0 + - - -
17A GLN 3.3 2.9 + - - -
18A ALA 3.4 1.5 + - - -
19A ALA* 2.8 33.6 + - - +
1353A NAP 3.0 35.1 + - - -
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Residues in contact with ARG 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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14A THR 3.7 1.0 + - - +
15A GLY* 1.3 72.5 - - - -
17A GLN* 1.3 62.9 + - - +
19A ALA* 4.2 4.3 - - - +
20A SER* 3.3 20.8 + - - -
153A TYR* 3.3 33.1 - - + -
155A ASN* 2.6 61.1 + - - +
156A ASN* 3.7 17.4 + - - +
192A ALA* 3.9 15.5 - - + +
193A GLU* 4.5 19.4 + - + +
1353A NAP 2.9 45.1 + - - +
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Residues in contact with GLN 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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16A ARG* 1.3 73.8 - - - +
18A ALA* 1.3 69.4 + - - +
20A SER* 3.2 5.9 + - - -
21A LEU 3.2 14.2 + - - -
78A PHE* 3.3 21.7 - - + -
80A ASN* 2.9 27.9 + - - +
111A SER* 2.6 25.9 + - - -
148A VAL* 5.2 0.3 - - - +
150A ALA* 3.7 23.0 - - + +
153A TYR* 2.9 27.1 + - + +
196A VAL* 3.6 32.0 - - + +
218A LEU* 5.9 2.2 - - - -
1353A NAP 3.0 19.1 + - - +
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Residues in contact with ALA 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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10A VAL* 3.5 28.0 - - + -
11A VAL 3.7 3.8 - - - +
12A ASN* 3.4 25.6 - - + +
13A ALA* 3.6 5.8 - - - +
15A GLY 3.4 1.6 + - - -
17A GLN* 1.3 78.2 - - - +
19A ALA* 1.3 66.6 + - - +
21A LEU* 2.9 4.7 + - - +
22A ILE* 2.8 26.5 + - + +
78A PHE* 3.7 15.3 - - + -
80A ASN* 5.4 2.6 - - + +
1353A NAP 4.5 1.0 + - - -
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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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13A ALA 3.1 13.9 + - - +
14A THR 4.1 6.1 - - - +
15A GLY 2.8 25.0 + - - +
16A ARG* 4.2 4.3 - - - +
18A ALA* 1.3 73.0 - - - +
20A SER* 1.3 62.4 + - - +
22A ILE* 3.4 6.8 + - - +
23A ARG* 3.0 52.6 + - - +
43A ILE* 4.5 9.0 - - + -
47A LEU* 4.5 4.7 - - + -
193A GLU* 6.4 0.2 - - + -
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Residues in contact with SER 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 ARG 3.3 13.2 + - - -
17A GLN 3.2 11.1 + - - -
18A ALA 3.0 0.6 + - - -
19A ALA* 1.3 82.2 - - - +
21A LEU* 1.3 65.8 + - - +
23A ARG* 3.4 12.6 + - - +
24A VAL* 3.3 22.2 + - - +
192A ALA 3.4 12.5 + - - -
193A GLU* 3.0 22.5 + - - -
196A VAL* 4.0 0.4 - - - -
197A GLY* 2.4 30.3 + - - -
198A PRO* 4.2 0.9 - - - +
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Residues in contact with LEU 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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8A ILE* 4.5 5.4 - - + -
10A VAL* 3.8 17.7 - - + -
17A GLN 3.2 7.0 + - - +
18A ALA 2.9 6.8 + - - +
20A SER* 1.3 78.0 - - - +
22A ILE* 1.3 57.4 + - - +
24A VAL* 3.1 6.7 + - + +
25A ALA* 2.6 49.5 + - + +
78A PHE* 3.3 41.3 - - + -
197A GLY* 3.5 16.1 - - - +
200A LEU* 4.1 28.5 - - + -
201A LEU* 4.6 5.6 - - + +
204A PHE* 4.2 20.2 - - + -
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Residues in contact with ILE 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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10A VAL* 4.4 14.1 - - + -
13A ALA* 3.7 44.0 - - + +
18A ALA 2.8 20.6 + - - +
19A ALA 3.6 4.5 - - - +
21A LEU* 1.3 70.6 - - - +
23A ARG* 1.3 65.5 + - - +
25A ALA* 4.3 5.2 - - - -
26A ALA* 2.8 24.8 + - - +
32A VAL* 4.1 16.6 - - + +
34A ALA* 4.1 14.1 - - + -
47A LEU* 3.5 24.5 - - + -
50A ILE* 4.6 1.6 - - + -
53A VAL* 3.9 25.8 - - + -
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Residues in contact with ARG 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 50.1 + - - +
20A SER* 3.4 13.9 - - - +
22A ILE* 1.3 75.6 - - - +
24A VAL* 1.3 65.0 + - + +
26A ALA* 4.0 1.2 - - - +
27A ALA* 3.0 25.6 + - - +
43A ILE* 3.8 18.6 - - - +
46A GLU* 2.7 35.1 + - - +
47A LEU* 4.9 4.0 - - + +
50A ILE* 4.1 20.5 - - + +
193A GLU* 4.8 18.2 + - - +
709I PRO* 3.7 19.1 - - + +
710I LEU 4.2 5.6 - - - -
711I SER* 3.3 40.3 - - - +
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Residues in contact with VAL 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 SER* 3.3 10.7 + - - +
21A LEU* 3.1 13.5 + - + +
23A ARG* 1.3 73.7 - - + +
25A ALA* 1.3 71.1 + - + +
27A ALA* 3.3 2.3 + - - +
28A VAL* 3.1 27.5 + - - +
193A GLU 6.0 0.7 - - - +
197A GLY* 3.6 34.5 - - - +
198A PRO* 4.2 9.9 - - + -
201A LEU* 3.8 15.3 - - + -
700I PHE* 3.9 23.1 - - + -
708I ARG* 5.8 1.8 - - + -
709I PRO* 3.6 23.3 - - + +
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Residues in contact with ALA 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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8A ILE* 3.9 26.9 - - + -
21A LEU* 2.6 31.2 + - + +
22A ILE* 3.8 2.7 - - - +
24A VAL* 1.3 77.6 - - - +
26A ALA* 1.3 63.9 + - - +
28A VAL* 3.4 7.5 - - - +
30A HIS* 3.0 36.5 + - + +
32A VAL* 4.2 10.1 - - + -
201A LEU* 5.0 3.4 - - + -
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Residues in contact with ALA 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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22A ILE 2.8 20.4 + - - +
23A ARG 4.0 1.3 - - - +
25A ALA* 1.3 73.2 - - - +
27A ALA* 1.3 64.8 + - - +
29A GLY* 3.0 14.7 + - - -
30A HIS 3.6 14.7 + - - +
32A VAL* 4.5 3.3 - - + +
50A ILE* 3.3 33.7 - - + -
52A ASN* 5.2 11.1 - - - +
53A VAL* 4.0 11.0 - - + -
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Residues in contact with ALA 27 (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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23A ARG 3.0 18.8 + - - +
24A VAL* 3.5 5.4 - - - +
26A ALA* 1.3 77.3 - - - +
28A VAL* 1.3 59.7 + - + +
50A ILE* 5.4 0.2 - - - +
706I VAL* 3.5 26.8 - - + +
707I VAL 5.0 1.3 - - - +
709I PRO* 3.8 27.8 - - + -
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Residues in contact with VAL 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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5A LYS* 3.3 26.0 - - + +
24A VAL 3.1 12.5 + - - +
25A ALA* 3.4 5.2 - - - +
27A ALA* 1.3 75.3 - - - +
29A GLY* 1.3 56.2 + - - +
30A HIS* 3.2 34.5 - - + +
201A LEU* 4.3 10.1 - - + -
700I PHE* 3.7 10.3 - - + -
704I HIS* 3.6 39.5 - - + +
706I VAL* 3.7 20.9 - - + +
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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