Contacts of the helix formed by residues 16 - 25 (chain B) in PDB entry 2VWE
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 SER 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLN* 4.0 5.2 - - - -
14B VAL* 3.4 7.6 + - - -
15B VAL* 1.3 75.2 - - - +
17B TRP* 1.3 60.5 + - - +
18B ILE* 3.2 16.5 + - - +
19B ASP* 2.9 29.3 + - - +
20B VAL* 2.9 23.9 + - - +
49J TYR* 3.4 12.3 + - - -
53J THR* 5.0 5.2 - - - -
54J LEU 4.1 13.8 + - - -
56J SER 5.9 0.3 + - - -
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Residues in contact with TRP 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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48A VAL* 3.1 25.1 + - + -
49A PRO* 3.7 9.9 - - + +
79A GLN* 3.0 55.6 + - + +
80A ILE* 4.0 0.7 - - - -
81A LEU* 3.7 11.6 - - + +
90A LEU* 3.5 22.7 - - + -
15B VAL 3.6 1.2 + - - -
16B SER* 1.3 72.6 + - - +
18B ILE* 1.3 60.4 + - + +
20B VAL* 3.2 3.2 + - + +
21B TYR* 3.0 55.8 + + - -
49J TYR* 3.6 17.0 + + - +
96L TYR* 3.5 35.2 - + + -
97L SER* 3.9 6.7 - - - -
100L VAL* 3.4 47.1 - + + -
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Residues in contact with ILE 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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16B SER* 3.2 8.3 + - - +
17B TRP* 1.3 81.5 - - + +
19B ASP* 1.3 60.8 + - - +
21B TYR* 3.5 31.7 - - + +
22B THR* 2.5 46.4 + - - +
46J LEU* 3.9 11.7 - - + -
49J TYR* 3.9 31.6 + - + -
54J LEU 5.9 0.2 - - - +
55J HIS* 3.4 39.9 - - + +
56J SER* 5.3 4.0 - - - +
94L ARG* 6.0 0.2 - - - +
100L ALA* 6.1 1.8 - - + +
101L ASP* 4.2 6.5 - - + +
102L TYR* 5.4 4.0 - - + +
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Residues in contact with ASP 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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53A THR* 5.4 0.9 + - - -
15B VAL* 3.9 16.1 - - + +
16B SER* 2.9 29.5 + - - +
18B ILE* 1.3 80.7 - - - +
20B VAL* 1.3 62.5 + - - +
22B THR* 4.3 5.0 - - - -
23B ARG* 4.1 19.4 + - - +
56J SER* 4.4 18.8 - - - -
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Residues in contact with VAL 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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49A PRO* 4.1 8.1 - - + -
52A VAL* 3.8 18.1 - - + -
53A THR* 4.8 4.6 + - - -
78A MET* 3.8 26.9 - - + -
79A GLN 3.6 14.1 - - - +
80A ILE* 3.8 28.5 - - + -
15B VAL* 3.8 16.2 - - + +
16B SER 2.9 17.8 + - - +
17B TRP* 3.3 9.9 - - - +
18B ILE 3.1 0.2 - - - -
19B ASP* 1.3 80.8 - - - +
21B TYR* 1.3 62.3 + - - +
23B ARG* 3.8 2.4 + - - +
24B ALA* 3.3 20.4 + - - +
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Residues in contact with TYR 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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49A PRO* 4.1 9.4 - - + -
17B TRP* 3.0 54.3 + + - +
18B ILE* 3.5 29.6 - - + +
20B VAL* 1.3 75.4 - - - +
22B THR* 1.3 68.8 + - - +
23B ARG 3.3 0.2 - - - -
24B ALA* 3.6 7.9 - - - -
25B THR* 2.5 39.5 + - - -
32L PHE* 3.4 24.7 - + - -
94L ARG* 4.5 1.1 - - - -
96L TYR* 3.6 51.7 + + + +
100L ALA 5.0 3.3 + - - -
101L ASP* 2.7 28.3 + - - +
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Residues in contact with THR 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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18B ILE* 2.5 34.1 + - - +
19B ASP* 4.5 6.7 + - - -
20B VAL 3.4 0.4 - - - -
21B TYR* 1.3 88.4 - - - +
23B ARG* 1.3 66.0 + - - +
24B ALA 3.7 0.2 + - - -
25B THR* 4.0 8.3 + - - -
27B GLN* 2.9 19.6 + - - +
32L PHE* 5.3 4.0 - - + -
94L ARG* 5.0 9.3 + - - +
102L TYR* 6.2 0.2 - - - -
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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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30A GLU* 2.8 37.4 + - - +
53A THR* 3.4 25.2 - - - +
19B ASP 4.1 13.1 + - - +
20B VAL 3.8 2.5 + - - +
22B THR* 1.3 84.6 - - - +
24B ALA* 1.3 55.0 + - - +
25B THR 3.4 0.4 - - - -
27B GLN* 3.3 31.4 + - - +
28B PRO 5.0 3.4 + - - -
29B ARG* 2.8 60.5 + - - +
30B GLU 5.9 0.2 - - - +
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Residues in contact with ALA 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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49A PRO* 3.7 16.6 - - + -
51A CYS* 3.2 32.1 - - - +
52A VAL* 4.3 4.0 - - - -
53A THR* 4.5 5.6 - - - +
20B VAL 3.3 19.3 + - - +
21B TYR 3.2 4.1 + - - +
23B ARG* 1.3 76.4 - - - +
25B THR* 1.3 65.5 + - - +
29B ARG* 4.1 0.9 - - - +
59B GLY* 3.5 4.6 - - - -
60B CYS 3.0 24.3 + - - +
96L TYR* 5.6 0.2 - - - -
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Residues in contact with THR 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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21B TYR 2.5 23.3 + - - -
22B THR 4.0 7.6 + - - -
23B ARG 3.4 0.8 - - - -
24B ALA* 1.3 78.7 - - - +
26B CYS* 1.3 77.0 + - + +
27B GLN* 3.0 9.5 + - - +
29B ARG* 2.8 24.1 + - - -
60B CYS 3.8 9.0 - - - +
62B PRO* 5.3 4.0 - - + -
103B CYS* 5.6 0.7 - - - -
28L THR* 4.7 8.1 - - + -
31L GLY* 4.7 14.4 - - - -
32L PHE* 3.7 33.6 - - + -
96L TYR* 3.8 13.8 + - + -
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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