Contacts of the helix formed by residues 15 - 23 (chain B) in PDB entry 3WTV
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 GLU 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 5.9 2.3 - - - -
11B LYS* 3.0 51.1 + - + +
14B ASN* 1.3 82.9 - - - +
16B GLU* 1.3 68.4 + - - +
17B PHE* 3.4 33.0 - - + +
18B PHE* 3.3 9.3 + - + +
19B ARG* 3.3 15.4 + - - +
104B ASN* 4.9 2.8 - - - +
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Residues in contact with GLU 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 ASN 3.3 3.6 + - - -
15B GLU* 1.3 74.8 - - + +
17B PHE* 1.3 64.5 + - - +
18B PHE 3.0 1.4 + - - -
19B ARG* 3.1 14.4 + - - +
20B LYS* 3.1 56.7 + - - +
359H ASP* 3.8 32.2 - - - +
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Residues in contact with PHE 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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66A ASP* 5.5 0.2 - - - -
161A THR* 3.8 22.2 - - + -
163A HIS* 3.5 30.7 - + + +
15B GLU* 3.3 25.8 - - + +
16B GLU* 1.3 79.0 - - - +
18B PHE* 1.3 70.8 + + + +
20B LYS* 4.3 5.5 + - - +
21B LEU* 3.1 52.5 + - + +
60B THR* 5.7 2.5 - - - -
62B THR* 3.9 20.0 - - + -
103B LEU* 3.4 25.1 - - + -
104B ASN* 3.4 25.6 - - - -
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Residues in contact with PHE 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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11B LYS* 3.3 47.1 - - + -
12B PHE* 3.7 40.0 - + + +
15B GLU* 3.3 9.0 + - + +
16B GLU 3.1 0.8 - - - -
17B PHE* 1.3 94.8 - + - +
19B ARG* 1.3 67.8 + - - +
20B LYS 3.2 1.8 - - - -
21B LEU* 2.8 15.3 + - + +
22B SER* 3.0 16.3 + - - -
103B LEU* 3.4 48.7 - - + -
104B ASN* 4.5 2.0 - - + -
106B VAL* 3.7 12.3 - - + -
108B VAL* 4.4 10.8 - - + -
125B LEU* 4.3 12.0 - - + +
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Residues in contact with ARG 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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12B PHE 4.7 5.2 - - - +
13B GLU* 3.1 24.0 + - - +
14B ASN* 3.0 29.3 + - - +
15B GLU 3.3 2.8 + - - +
16B GLU* 3.1 18.9 + - - +
18B PHE* 1.3 78.1 - - - +
20B LYS* 1.3 61.3 + - - +
21B LEU 3.2 1.0 + - - -
22B SER* 3.2 21.9 + - - -
23B ARG* 4.0 11.4 + - - +
427H GLU* 3.5 29.9 + - - +
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Residues in contact with LYS 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 GLU* 3.1 49.6 + - - +
17B PHE* 4.7 5.0 + - - +
19B ARG* 1.3 76.2 - - - +
21B LEU* 1.3 61.9 + - + +
22B SER 3.5 0.2 - - - -
23B ARG* 4.7 8.4 - - - +
25B CYS* 3.0 21.8 - - - -
59B ALA* 6.4 3.4 - - + -
60B THR* 4.4 25.4 - - - +
359H ASP* 4.7 15.3 + - - +
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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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17B PHE* 3.1 48.7 - - + +
18B PHE* 2.8 10.3 + - + +
20B LYS* 1.3 82.7 - - + +
22B SER* 1.3 61.3 + - - +
23B ARG 3.5 4.2 - - - +
25B CYS* 3.9 3.6 - - - -
57B PHE* 3.3 41.1 - - + -
60B THR* 3.7 22.0 - - + +
62B THR* 4.9 4.7 - - + +
64B LEU* 6.3 0.9 - - + -
103B LEU* 5.1 1.6 - - + -
124B CYS* 3.6 7.4 - - - -
125B LEU* 3.2 46.0 + - + -
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Residues in contact with SER 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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12B PHE* 3.7 25.3 + - - -
18B PHE 3.0 13.6 + - - -
19B ARG* 3.2 13.2 + - - -
21B LEU* 1.3 75.9 - - - +
23B ARG* 1.3 70.7 + - - +
24B GLU* 5.0 0.2 - - - +
124B CYS* 3.1 18.4 - - - +
125B LEU* 4.2 11.9 - - - +
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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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19B ARG 4.0 11.9 + - - +
20B LYS* 5.0 6.5 - - - +
21B LEU 3.5 0.4 - - - +
22B SER* 1.3 84.9 - - - +
24B GLU* 1.3 55.3 + - - +
25B CYS* 2.6 34.0 + - - +
124B CYS* 3.5 7.1 - - - +
357H THR 4.9 10.7 + - - -
358H GLY* 5.5 6.1 + - - -
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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