Contacts of the helix formed by residues 19 - 29 (chain A) in PDB entry 5WZF
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 ARG 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 4.0 3.1 - - + -
17A ASP* 2.7 19.6 + - - +
18A ALA* 1.3 98.4 + - + +
20A HIS* 1.3 57.2 + - - +
21A GLY 3.3 2.5 - - - -
22A THR* 2.3 36.4 + - - +
23A ALA* 2.9 28.9 + - - +
116A PHE* 4.0 39.4 - - + -
117A ASP* 5.3 4.0 - - - +
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.8 29.3 + - - +
12A LEU* 3.1 20.9 + - + -
14A ASN 3.4 12.1 + - - +
15A ALA* 3.6 33.4 - - + +
17A ASP* 3.1 20.5 + - - +
18A ALA 3.4 0.4 - - - -
19A ARG* 1.3 76.7 - - - +
21A GLY* 1.3 58.7 + - - +
23A ALA* 3.3 2.3 + - - +
24A LYS* 2.9 70.2 + - + +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA 4.8 2.2 + - - -
19A ARG 3.3 0.8 - - - -
20A HIS* 1.3 80.8 - - - +
22A THR* 1.3 60.5 + - - +
24A LYS* 3.4 16.6 + - - +
25A ARG* 3.2 21.7 + - - +
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Residues in contact with THR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 2.3 46.9 + - - +
21A GLY* 1.3 74.1 - - - +
23A ALA* 1.3 66.5 + - - +
25A ARG* 3.3 5.9 + - - +
26A LEU* 3.0 27.5 + - + +
116A PHE* 3.9 20.6 - - + -
129A ARG* 4.9 5.2 - - - -
130A PRO* 3.9 27.4 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.3 29.1 - - + -
11A ALA* 3.9 7.2 - - + -
12A LEU* 3.8 30.3 - - - +
19A ARG 2.9 16.8 + - - +
20A HIS 3.5 4.9 - - - +
22A THR* 1.3 77.7 - - - +
24A LYS* 1.3 58.4 + - - +
26A LEU 3.4 0.5 + - - -
27A TRP* 2.9 30.8 + - - +
116A PHE* 4.2 3.5 - - + -
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.9 14.1 - - + -
20A HIS* 2.9 55.3 + - + +
21A GLY* 3.6 11.9 - - - +
22A THR 3.3 0.2 - - - -
23A ALA* 1.3 77.0 - - - +
25A ARG* 1.3 61.9 + - - +
27A TRP* 3.4 2.9 + - - +
28A ALA* 3.1 23.9 + - - +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY 3.2 11.2 + - - +
22A THR* 3.8 7.6 - - - +
24A LYS* 1.3 78.3 - - - +
26A LEU* 1.3 61.8 + - - +
28A ALA* 3.2 16.1 + - + +
29A SER* 3.3 15.8 + - - +
130A PRO* 3.8 38.4 + - + +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.8 23.1 - - + -
22A THR* 3.0 34.1 + - + +
23A ALA 3.7 3.8 - - - +
25A ARG* 1.3 76.7 - - - +
27A TRP* 1.3 62.7 + - - +
29A SER* 3.2 9.4 + - - +
30A LYS 3.1 10.0 + - - -
114A TYR* 2.8 36.2 + - + +
115A ALA 6.0 0.2 - - - +
116A PHE* 4.4 8.5 - - + -
128A VAL* 3.5 34.3 - - + +
129A ARG* 3.9 7.0 - - - +
130A PRO* 3.6 30.3 - - + -
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Residues in contact with TRP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.4 5.6 - - + -
8A PHE* 3.5 22.6 - + - -
9A TRP* 3.4 39.5 - + - -
12A LEU* 3.7 26.3 - - + +
23A ALA 2.9 18.4 + - - +
24A LYS* 3.6 5.4 - - - +
26A LEU* 1.3 76.2 - - - +
28A ALA* 1.3 62.1 + - - +
30A LYS* 3.1 63.6 - - + +
34A VAL* 4.2 17.0 - - + -
68A VAL* 6.2 0.2 - - + -
69A VAL* 4.3 9.2 - - + -
114A TYR* 4.3 6.5 - + - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS 3.1 13.1 + - - +
25A ARG* 3.5 11.7 - - + +
26A LEU 3.2 0.4 - - - -
27A TRP* 1.3 78.9 - - - +
29A SER* 1.3 57.3 + - - +
30A LYS* 3.5 2.2 + - - +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.3 16.0 + - - +
26A LEU* 3.2 14.8 + - - +
28A ALA* 1.3 79.0 - - - +
30A LYS* 1.3 63.8 + - - +
31A PRO* 3.8 2.3 - - - +
114A TYR* 3.9 4.4 + - - -
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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