Contacts of the helix formed by residues 18 - 24 (chain C) in PDB entry 3WA9
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 18 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA 4.0 2.0 + - - -
17C VAL* 1.3 79.2 - - - +
19C ARG* 1.3 58.7 + - - +
20C SER* 3.6 9.4 + - - -
21C GLN* 3.1 30.4 + - - +
22C ARG* 2.8 23.8 + - - +
29I A 5.1 0.9 - - - -
30I A 3.6 17.7 - - - -
267J G 5.4 13.5 - - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 1.3 69.6 - - - +
20C SER* 1.3 60.0 + - - +
22C ARG* 3.3 19.7 + - - +
23C ALA* 2.9 29.3 + - - +
29C VAL* 3.9 31.8 - - + +
30C GLY* 3.7 13.3 + - - +
33C HIS* 3.2 44.6 + - - +
48C ALA* 4.0 17.2 + - - +
51C ALA* 4.6 0.6 - - - +
121D TYR* 3.1 33.8 + - + +
30I A 2.7 41.4 + - - +
31I G 5.8 0.4 - - - +
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.9 8.1 + - - -
19C ARG* 1.3 75.3 + - - +
21C GLN* 1.3 57.7 + - - +
23C ALA* 2.8 21.0 + - - +
24C GLY 2.8 11.8 + - - -
25C LEU* 3.0 21.5 + - - -
26C GLN 5.2 1.1 - - - -
27C PHE 3.0 25.9 + - - -
28C PRO* 3.5 5.4 - - - +
29C VAL* 3.1 23.8 + - - +
30C GLY 4.8 1.0 + - - -
30I A 4.4 1.2 + - - -
268J G 5.7 0.3 + - - -
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ALA 5.1 0.7 - - - +
17C VAL* 3.8 25.0 - - + +
18C SER* 3.1 26.6 + - - +
20C SER* 1.3 77.4 - - - +
22C ARG* 1.3 64.1 + - - +
24C GLY* 3.0 14.6 + - - +
25C LEU 4.3 3.8 + - - +
120D LYS* 4.0 7.1 + - - -
267J G 5.6 4.4 + - - -
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 3.1 44.7 + - + +
18C SER 2.8 17.4 + - - +
19C ARG* 3.4 18.6 - - - +
20C SER 3.2 0.2 - - - -
21C GLN* 1.3 75.5 - - - +
23C ALA* 1.3 56.5 + - - +
120D LYS* 3.5 29.9 + - - +
121D TYR* 3.8 37.1 - - + +
124D ALA* 3.7 30.7 + - - +
31I G 3.7 27.7 + - - -
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG 2.9 14.8 + - - +
20C SER 2.8 6.0 + - - +
22C ARG* 1.3 76.3 - - - +
24C GLY* 1.3 63.9 + - - +
25C LEU* 3.5 26.4 - - + +
29C VAL* 4.5 2.5 - - + -
52C VAL* 3.8 20.9 - - + -
117D ALA* 3.8 21.3 - - - +
120D LYS* 3.6 13.2 - - - +
121D TYR* 4.2 6.5 - - + -
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER 2.8 2.7 + - - -
21C GLN* 3.0 12.8 + - - -
22C ARG 3.4 0.6 - - - -
23C ALA* 1.3 80.2 - - - +
25C LEU* 1.3 66.0 + - - +
26C GLN* 5.4 3.6 + - - -
59C GLU* 4.6 2.8 - - - +
120D LYS* 3.8 16.0 - - - +
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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
------------------------------------------------------------
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