Contacts of the helix formed by residues 15 - 29 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN* 2.8 20.4 + - - +
14B THR* 1.3 81.3 + - - +
16B ARG* 1.3 60.7 + - - -
17B GLN 3.3 0.4 - - - -
18B ALA 4.1 1.8 - - - -
19B ALA* 2.9 28.8 + - - +
1353B NAP 3.1 33.3 + - - -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR 3.7 1.3 + - - +
15B GLY* 1.3 71.2 - - - -
17B GLN* 1.3 61.2 + - - +
19B ALA* 4.3 3.5 - - - +
20B SER* 3.2 24.8 + - - -
23B ARG* 5.2 0.3 + - - -
153B TYR* 3.1 23.6 - - - -
155B ASN* 2.9 51.8 + - - +
156B ASN* 3.5 18.2 + - - +
192B ALA* 3.9 21.1 - - + +
193B GLU* 4.7 9.3 - - + +
1353B NAP 2.6 54.6 + - - +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 1.3 78.8 - - - +
18B ALA* 1.3 61.4 + - - +
20B SER* 3.4 3.5 - - - -
21B LEU* 3.3 18.9 + - - +
78B PHE* 3.4 24.1 - - + -
80B ASN* 3.3 20.1 + - - +
111B SER* 2.9 26.0 + - - -
150B ALA* 3.9 19.7 - - - +
153B TYR* 2.7 32.2 + - + +
192B ALA* 5.1 0.4 - - + -
196B VAL* 3.7 31.7 - - + +
218B LEU* 5.3 4.4 - - - +
1353B NAP 2.9 19.5 + - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.5 26.7 - - + -
11B VAL 3.8 3.4 - - - +
12B ASN* 3.2 27.1 - - + +
13B ALA* 3.7 7.9 - - - -
15B GLY 3.5 1.8 + - - -
17B GLN* 1.3 77.1 - - - +
19B ALA* 1.3 66.6 + - - +
21B LEU* 3.2 3.6 + - - +
22B ILE* 2.8 26.5 + - - +
78B PHE* 3.9 13.6 - - + -
80B ASN* 5.3 3.5 - - + +
1353B NAP 4.5 0.4 + - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 3.2 14.2 + - - +
14B THR 4.4 0.4 - - - +
15B GLY 2.9 24.1 + - - +
16B ARG* 4.3 3.4 - - - +
18B ALA* 1.3 71.9 - - - +
20B SER* 1.3 64.0 + - - +
22B ILE* 3.1 6.6 + - - +
23B ARG* 2.9 53.2 + - - +
43B ILE* 4.3 14.6 - - + -
47B LEU* 4.4 5.2 - - + -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG 3.2 18.3 + - - -
17B GLN 3.4 5.8 - - - -
19B ALA* 1.3 80.5 - - - +
21B LEU* 1.3 62.6 + - - +
23B ARG* 3.5 14.9 - - - +
24B VAL* 3.0 25.1 + - - +
192B ALA 3.4 14.9 + - - -
193B GLU* 3.3 19.4 + - - -
196B VAL* 4.0 0.7 - - - -
197B GLY* 2.4 31.9 + - - -
198B PRO* 4.3 0.9 - - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 4.5 6.5 - - + -
10B VAL* 4.4 15.3 - - + -
17B GLN 3.3 8.8 + - - +
18B ALA 3.2 7.2 + - - +
20B SER* 1.3 80.1 - - - +
22B ILE* 1.3 54.4 + - + +
24B VAL* 2.8 9.0 - - + +
25B ALA* 2.6 54.2 + - + +
78B PHE* 3.4 37.9 - - + -
197B GLY* 3.6 10.9 - - - +
200B LEU* 4.0 28.3 - - + -
201B LEU* 4.6 8.1 - - + +
204B PHE* 4.4 16.6 - - + -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.4 11.9 - - + -
13B ALA* 3.7 37.2 - - + +
18B ALA 2.8 21.0 + - - +
19B ALA 3.6 4.3 - - - +
21B LEU* 1.3 74.3 - - - +
23B ARG* 1.3 68.1 + - - +
25B ALA* 4.0 3.5 - - - +
26B ALA* 2.8 24.8 + - - +
32B VAL* 3.8 18.3 - - + +
34B ALA* 3.9 15.9 - - + -
47B LEU* 3.7 23.3 - - + -
50B ILE* 4.3 2.0 - - + -
53B VAL* 3.8 28.5 - - + -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG 5.2 0.4 + - - -
19B ALA* 2.9 34.3 + - - +
20B SER* 3.5 32.9 - - - +
22B ILE* 1.3 76.8 - - - +
24B VAL* 1.3 65.0 + - + +
26B ALA* 3.9 1.4 - - - +
27B ALA* 3.0 23.0 + - - +
43B ILE* 3.9 21.8 - - - +
46B GLU* 2.8 26.5 + - - +
47B LEU* 4.6 3.3 - - + +
50B ILE* 4.3 19.4 - - + +
193B GLU* 4.4 20.8 + - - +
709J PRO* 3.8 17.7 - - + +
710J LEU* 3.6 22.7 - - - +
711J SER* 3.7 21.1 - - - -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER* 3.0 15.7 - - - +
21B LEU* 2.8 26.9 - - + +
23B ARG* 1.3 81.1 - - + +
25B ALA* 1.3 62.1 + - - +
27B ALA* 3.4 1.0 + - - +
28B VAL* 3.1 29.9 + - - +
197B GLY* 3.4 22.7 - - - +
198B PRO* 4.1 16.8 - - + -
201B LEU* 4.1 14.4 - - + -
700J PHE* 3.8 17.0 - - + -
708J ARG* 5.7 2.7 - - + +
709J PRO* 3.6 24.9 - - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 3.5 32.1 - - + -
21B LEU* 2.6 32.4 + - + +
22B ILE 4.0 2.0 - - - +
24B VAL* 1.3 74.2 - - - +
26B ALA* 1.3 61.2 + - - +
28B VAL* 3.5 1.1 + - - -
29B GLY 3.4 4.2 + - - -
30B HIS* 2.9 38.8 + - + +
32B VAL* 4.4 7.0 - - + -
201B LEU* 4.7 5.4 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE 2.8 20.4 + - - +
23B ARG 3.9 1.1 - - - +
25B ALA* 1.3 72.5 - - - +
27B ALA* 1.3 65.0 + - - +
29B GLY* 3.0 15.2 + - - -
30B HIS 3.7 14.4 + - - +
32B VAL* 4.5 3.5 - - + +
50B ILE* 3.4 32.3 - - + -
52B ASN* 4.7 13.1 - - + +
53B VAL* 4.0 11.4 - - + -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG 3.0 18.2 + - - +
24B VAL 3.7 4.9 - - - +
25B ALA 3.3 0.2 - - - -
26B ALA* 1.3 77.8 - - - +
28B VAL* 1.3 60.3 + - + +
29B GLY 3.6 0.2 + - - -
50B ILE* 5.4 0.4 - - - +
706J VAL* 3.4 31.5 - - + +
709J PRO* 3.7 27.4 - - + -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 3.3 24.1 - - - +
24B VAL 3.1 15.5 + - - +
25B ALA* 3.6 2.9 - - - +
26B ALA 3.2 0.4 - - - -
27B ALA* 1.3 75.8 - - - +
29B GLY* 1.3 56.8 + - - +
30B HIS* 3.1 37.5 - - + +
201B LEU* 4.0 11.0 - - + -
700J PHE* 3.8 25.8 - - + -
704J HIS* 4.0 27.5 - - + +
706J VAL* 4.4 10.6 - - + +
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 3.1 22.9 - - - +
26B ALA 3.0 11.3 + - - -
27B ALA 3.3 1.2 + - - -
28B VAL* 1.3 81.8 - - - +
30B HIS* 1.3 63.3 + - - +
31B HIS* 4.4 8.5 + - - -
52B ASN* 5.7 3.6 - - - -
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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