Contacts of the helix formed by residues 15 - 29 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASN* 2.7 25.6 + - - -
14G THR* 1.3 75.5 - - - +
16G ARG* 1.3 60.2 + - - -
17G GLN 3.3 2.9 - - - -
18G ALA* 4.2 1.3 - - - -
19G ALA* 3.0 28.3 + - - +
1353G NAP 3.1 32.4 + - - -
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Residues in contact with ARG 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G THR 5.5 0.7 - - - +
15G GLY* 1.3 69.7 - - - -
17G GLN* 1.3 68.3 + - - +
19G ALA* 4.6 1.7 - - - +
20G SER* 3.3 20.3 + - - -
153G TYR* 3.2 24.4 - - + -
155G ASN* 2.9 55.2 + - - +
156G ASN* 3.8 13.7 + - - +
192G ALA* 3.9 22.3 - - + +
193G GLU* 4.0 22.6 + - + +
1353G NAP 2.9 48.9 + - - +
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Residues in contact with GLN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ARG* 1.3 73.7 - - + +
18G ALA* 1.3 68.9 + - - +
20G SER* 3.0 19.6 + - - -
21G LEU* 3.2 4.7 + - - +
78G PHE* 3.5 18.8 - - + -
80G ASN* 3.0 23.6 + - - +
111G SER* 2.7 27.3 + - - -
150G ALA* 4.3 12.3 - - + +
153G TYR* 2.7 31.7 + - + +
192G ALA* 5.4 0.4 - - + -
196G VAL* 3.7 30.0 - - + +
218G LEU* 6.0 2.6 - - - +
1353G NAP 3.1 26.0 + - - +
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 3.7 18.2 - - + -
11G VAL 3.8 4.0 - - - +
12G ASN* 3.3 29.2 - - - +
13G ALA* 3.5 13.7 - - - +
15G GLY* 3.7 1.5 + - - +
17G GLN* 1.3 77.6 - - - +
19G ALA* 1.3 52.0 + - - +
21G LEU* 2.9 5.4 + - - +
22G ILE* 2.8 37.4 + - - +
78G PHE* 3.9 16.0 - - + -
80G ASN* 5.4 1.1 - - + +
1353G NAP 4.5 0.4 + - - -
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Residues in contact with ALA 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ALA 3.0 12.9 + - - +
14G THR 4.4 0.4 - - - +
15G GLY 3.0 24.2 + - - +
16G ARG* 4.6 2.7 - - - +
18G ALA* 1.3 73.5 - - - +
20G SER* 1.3 56.2 + - - +
22G ILE* 3.7 6.8 - - - +
23G ARG* 3.0 53.9 + - - +
43G ILE* 4.1 19.7 - - + -
47G LEU* 4.4 5.1 - - + +
193G GLU* 5.5 1.8 - - - +
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Residues in contact with SER 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ARG 3.3 13.8 + - - -
17G GLN 3.0 11.7 + - - -
19G ALA* 1.3 75.1 - - - +
21G LEU* 1.3 65.7 + - - +
23G ARG* 3.8 10.4 - - - +
24G VAL* 3.0 29.6 + - - +
192G ALA 3.0 12.8 + - - -
193G GLU* 2.9 28.4 + - - +
196G VAL* 3.9 0.8 + - - -
197G GLY* 3.0 23.9 + - - -
198G PRO* 4.5 1.4 - - - +
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Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 4.4 13.9 - - + -
10G VAL* 4.6 8.3 - - + -
17G GLN 3.2 6.1 + - - +
18G ALA* 2.9 10.4 + - - +
20G SER* 1.3 78.7 - - - +
22G ILE* 1.3 56.5 + - + +
24G VAL* 3.1 2.8 + - + +
25G ALA* 2.6 50.6 + - + +
78G PHE* 3.6 34.1 - - + -
197G GLY* 3.5 15.6 - - - +
200G LEU* 3.9 31.4 - - + -
201G LEU* 4.3 11.9 - - + +
204G PHE* 4.2 15.7 - - + -
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Residues in contact with ILE 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 4.3 15.7 - - + -
13G ALA* 3.8 36.3 - - + +
18G ALA 2.8 22.8 + - - +
19G ALA* 3.7 5.6 - - - +
21G LEU* 1.3 74.4 - - + +
23G ARG* 1.3 63.7 + - - +
25G ALA* 4.0 4.9 - - - +
26G ALA* 2.9 24.8 + - - +
32G VAL* 3.8 18.5 - - + +
34G ALA* 3.8 16.2 - - + -
47G LEU* 4.0 20.4 - - + -
50G ILE* 4.6 1.6 - - + -
53G VAL* 3.9 27.8 - - + -
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Residues in contact with ARG 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ALA* 3.0 51.8 + - - +
20G SER* 3.8 9.2 - - - +
22G ILE* 1.3 74.5 - - - +
24G VAL* 1.3 60.6 + - + +
26G ALA* 4.0 1.6 - - - +
27G ALA* 3.0 30.5 + - - +
43G ILE* 3.8 14.8 - - - +
46G GLU* 2.8 43.8 + - - +
47G LEU* 4.9 2.2 - - + +
50G ILE* 4.3 20.7 - - + +
193G GLU* 4.5 16.0 + - - +
709O PRO* 3.6 17.2 - - + +
710O LEU* 3.1 28.1 + - - +
711O SER 3.1 23.9 + - - -
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G SER* 3.0 16.8 - - - +
21G LEU 3.1 6.7 + - - +
23G ARG* 1.3 73.8 - - + +
25G ALA* 1.3 64.9 + - - +
27G ALA* 3.4 2.1 + - - +
28G VAL* 3.2 25.8 + - - +
193G GLU 6.0 0.4 - - - +
197G GLY* 3.9 11.4 - - - +
198G PRO* 3.8 22.0 - - + -
201G LEU* 3.4 28.3 - - + -
700O PHE* 3.4 23.7 - - + -
708O ARG* 6.0 1.1 - - + -
709O PRO* 3.6 20.0 - - + +
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 3.6 30.3 - - + -
21G LEU* 2.6 31.0 + - + +
22G ILE* 4.0 2.2 - - - +
24G VAL* 1.3 73.5 - - - +
26G ALA* 1.3 62.0 + - - +
28G VAL* 3.0 17.0 - - - +
30G HIS* 3.0 30.7 + - + +
32G VAL* 4.3 8.3 - - + -
201G LEU* 4.8 3.4 - - + -
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ILE 2.9 18.8 + - - +
23G ARG 4.0 1.1 - - - +
25G ALA* 1.3 76.5 - - - +
27G ALA* 1.3 63.1 + - - +
29G GLY* 3.1 14.4 + - - -
30G HIS 3.7 14.6 + - - +
32G VAL* 4.4 3.1 - - + +
50G ILE* 3.4 31.2 - - + -
52G ASN* 4.6 12.5 - - + +
53G VAL* 4.0 11.9 - - + -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ARG 3.0 20.1 + - - +
24G VAL 3.6 3.4 - - - +
25G ALA 3.3 0.2 - - - -
26G ALA* 1.3 77.4 - - - +
28G VAL* 1.3 58.9 + - + +
29G GLY 3.4 0.3 + - - -
50G ILE* 5.4 0.6 - - - +
706O VAL* 3.7 24.8 - - + +
707O VAL 4.8 1.3 - - - +
709O PRO* 3.6 31.0 - - + -
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Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 3.7 26.8 + - + +
24G VAL 3.3 13.0 - - - +
25G ALA* 3.0 20.6 - - - +
27G ALA* 1.3 77.1 - - - +
29G GLY* 1.3 56.4 + - - +
30G HIS* 3.3 23.6 - - + +
201G LEU* 4.0 11.2 - - + -
700O PHE* 3.9 7.9 - - + -
704O HIS* 3.5 40.7 - - + +
706O VAL* 3.7 19.1 - - + +
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Residues in contact with GLY 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LYS* 3.2 22.7 - - - +
26G ALA 3.1 10.7 + - - -
27G ALA 3.3 1.2 + - - -
28G VAL* 1.3 80.5 - - - +
30G HIS* 1.3 63.6 + - - +
31G HIS* 4.1 10.6 + - - -
52G ASN* 4.9 7.9 - - - +
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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