Contacts of the helix formed by residues 15 - 29 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F ASN* 2.8 16.4 + - - -
14F THR* 1.3 80.4 - - - +
16F ARG* 1.3 59.7 + - - -
17F GLN 3.2 3.4 + - - -
18F ALA 3.3 2.2 + - - -
19F ALA* 2.8 27.8 + - - +
1353F NAP 3.0 34.9 + - - -
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Residues in contact with ARG 16 (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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14F THR 3.7 1.0 + - - +
15F GLY* 1.3 71.2 - - - -
17F GLN* 1.3 64.1 + - - +
19F ALA* 4.4 3.5 - - - +
20F SER* 3.3 22.0 + - - -
23F ARG* 6.2 0.7 - - - +
153F TYR* 3.2 28.1 - - + -
155F ASN* 2.5 62.9 + - - +
156F ASN* 3.9 11.9 + - - +
192F ALA* 3.9 21.6 - - + +
193F GLU* 4.4 18.4 + - + +
1353F NAP 2.8 44.7 + - - +
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Residues in contact with GLN 17 (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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16F ARG* 1.3 78.8 - - - +
18F ALA* 1.3 63.5 + - - +
20F SER* 3.3 13.9 - - - -
21F LEU* 3.3 7.3 + - - +
78F PHE* 3.8 21.6 - - + -
80F ASN* 2.8 35.2 + - - +
111F SER* 2.9 23.2 + - - -
150F ALA* 4.1 11.9 - - + +
153F TYR* 2.9 31.4 + - + +
192F ALA* 5.3 0.2 - - + -
196F VAL* 3.7 28.8 - - + +
218F LEU* 5.3 3.6 - - - +
1353F NAP 3.1 20.7 + - - +
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Residues in contact with ALA 18 (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 VAL* 4.5 9.2 - - + -
11F VAL 3.7 13.9 - - - +
12F ASN* 3.4 26.5 - - + +
13F ALA* 3.7 10.5 - - - -
15F GLY 3.3 1.8 + - - -
17F GLN* 1.3 77.0 - - - +
19F ALA* 1.3 60.0 + - - +
21F LEU* 3.1 4.5 + - - +
22F ILE* 2.8 33.2 + - - +
78F PHE* 4.1 17.4 - - + -
80F ASN* 5.6 2.4 - - + +
1353F NAP 4.4 0.8 + - - +
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Residues in contact with ALA 19 (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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13F ALA 3.2 14.7 + - - +
14F THR 4.5 0.4 - - - +
15F GLY 2.8 22.4 + - - +
16F ARG* 4.4 2.9 - - - +
18F ALA* 1.3 73.4 - - - +
20F SER* 1.3 63.0 + - - +
22F ILE* 3.7 6.1 - - - +
23F ARG* 2.9 53.7 + - - +
43F ILE* 4.3 15.9 - - + -
47F LEU* 4.3 5.8 - - + -
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Residues in contact with SER 20 (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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16F ARG 3.3 14.2 + - - -
17F GLN 3.3 11.4 + - - -
18F ALA 3.1 0.4 - - - -
19F ALA* 1.3 78.9 - - - +
21F LEU* 1.3 63.1 + - - +
23F ARG* 3.4 14.0 - - - +
24F VAL* 3.1 28.9 + - - +
192F ALA 3.0 12.8 + - - -
193F GLU* 2.9 23.1 + - - -
196F VAL* 4.1 0.9 - - - -
197F GLY* 2.7 26.6 + - - -
198F PRO* 4.5 0.9 - - - +
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Residues in contact with LEU 21 (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 ILE* 4.4 15.7 - - + -
10F VAL* 3.8 21.1 - - + -
17F GLN 3.3 7.5 + - - +
18F ALA* 3.1 8.0 + - - +
20F SER* 1.3 79.8 - - - +
22F ILE* 1.3 56.2 + - + +
24F VAL* 3.2 1.6 + - - +
25F ALA* 2.6 53.0 + - + +
78F PHE* 3.4 37.2 - - + -
197F GLY* 3.5 14.8 - - - +
200F LEU* 4.2 27.6 - - + -
201F LEU* 4.8 9.4 - - + +
204F PHE* 4.7 6.7 - - + -
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Residues in contact with ILE 22 (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 VAL* 3.5 37.0 - - + -
13F ALA* 3.7 26.5 - - + +
18F ALA 2.8 24.1 + - - +
19F ALA* 3.7 4.7 - - - +
21F LEU* 1.3 73.6 - - - +
23F ARG* 1.3 64.6 + - - +
25F ALA* 3.9 3.8 - - - +
26F ALA* 2.9 24.3 + - - +
32F VAL* 4.1 13.7 - - + -
34F ALA* 4.0 8.5 - - + -
47F LEU* 4.4 17.7 - - + -
50F ILE* 4.7 2.5 - - + -
53F VAL* 3.7 29.6 - - + -
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Residues in contact with ARG 23 (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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16F ARG* 5.3 1.0 + - - +
19F ALA* 2.9 52.9 + - - +
20F SER* 3.4 21.8 - - - +
22F ILE* 1.3 75.1 - - - +
24F VAL* 1.3 64.8 + - + +
26F ALA* 4.2 1.2 - - - +
27F ALA* 3.1 25.3 + - - +
43F ILE* 4.1 14.1 - - - +
46F GLU* 2.6 27.2 + - - +
47F LEU* 4.9 3.1 - - + +
50F ILE* 4.2 23.3 - - + +
193F GLU* 3.3 32.9 + - - +
709N PRO* 3.7 17.1 - - + +
710N LEU 3.2 24.5 - - - -
711N SER* 3.6 15.2 + - - -
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Residues in contact with VAL 24 (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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20F SER* 3.1 18.8 - - - +
21F LEU 3.2 2.6 + - - +
23F ARG* 1.3 74.8 - - + +
25F ALA* 1.3 66.0 + - - +
27F ALA* 3.3 2.6 + - - +
28F VAL* 3.1 23.9 + - - +
193F GLU 5.9 1.1 - - - +
197F GLY 4.4 3.8 - - - -
198F PRO* 3.9 28.5 - - + -
201F LEU* 2.9 32.8 - - + -
700N PHE* 3.3 23.6 - - + -
708N ARG* 5.9 1.3 - - + -
709N PRO* 3.6 20.6 - - + +
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Residues in contact with ALA 25 (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 ILE* 4.0 19.5 - - + -
21F LEU* 2.6 37.8 + - + +
22F ILE 3.9 2.0 - - - +
24F VAL* 1.3 75.3 - - - +
26F ALA* 1.3 64.2 + - - +
28F VAL* 3.2 9.7 + - - +
30F HIS* 3.1 34.2 + - + +
32F VAL* 4.3 9.9 - - + -
201F LEU* 4.5 4.9 - - + +
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Residues in contact with ALA 26 (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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22F ILE 2.9 21.0 + - - +
23F ARG 4.2 0.7 - - - +
25F ALA* 1.3 73.0 - - - +
27F ALA* 1.3 65.3 + - - +
29F GLY* 2.9 16.5 + - - -
30F HIS 3.6 14.8 - - - +
32F VAL* 4.8 3.3 - - + +
50F ILE* 3.4 31.0 - - + -
52F ASN* 5.1 9.7 - - + +
53F VAL* 4.0 12.1 - - + -
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Residues in contact with ALA 27 (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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23F ARG 3.1 18.4 + - - +
24F VAL 3.5 4.9 - - - +
25F ALA 3.3 0.2 - - - -
26F ALA* 1.3 78.7 - - - +
28F VAL* 1.3 61.0 + - + +
29F GLY 3.4 0.2 + - - -
50F ILE* 5.4 0.8 - - - +
706N VAL* 3.9 23.3 - - + +
707N VAL 5.0 1.6 - - - +
709N PRO* 3.8 26.0 - - + -
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Residues in contact with VAL 28 (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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5F LYS* 3.2 25.8 - - - +
24F VAL 3.1 14.3 + - - +
25F ALA* 3.3 4.9 - - - +
27F ALA* 1.3 75.1 - - - +
29F GLY* 1.3 56.8 + - - +
30F HIS* 3.1 35.9 - - + +
201F LEU* 4.2 9.9 - - + -
700N PHE* 3.7 26.0 - - + -
704N HIS* 3.8 25.1 - - + +
706N VAL* 3.8 16.7 - - + +
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Residues in contact with GLY 29 (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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5F LYS* 3.3 23.7 - - - +
26F ALA 2.9 11.3 + - - -
27F ALA 3.3 1.4 + - - -
28F VAL* 1.3 80.9 - - - +
30F HIS* 1.3 63.5 + - - +
31F HIS* 4.3 9.6 + - - -
52F ASN* 6.2 1.3 - - - -
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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