Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 2QXU
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 PHE 19 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 3.5 47.8 - - + -
9C VAL 3.4 21.5 - - - -
10C HIS* 3.6 29.2 - - + -
15C ALA 4.1 10.5 - - - -
16C SER* 3.3 15.4 + - - +
17C PHE 3.0 1.2 - - - -
18C ASN* 1.3 80.2 - - + +
20C ALA* 1.3 63.5 + - - +
21C GLY 3.2 2.7 - - - -
22C ILE* 3.0 33.9 + - + +
23C LYS* 2.8 25.5 + - - +
38C ALA* 5.1 0.2 - - + -
74C VAL* 3.8 20.6 - - + -
76C HIS* 4.1 14.6 - - + -
102C LEU* 4.8 0.7 - - + -
160C LEU* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C SER 4.1 1.6 + - - -
17C PHE* 3.0 21.1 + - + +
18C ASN 3.3 0.6 - - - -
19C PHE* 1.3 75.9 - - - +
21C GLY* 1.3 63.2 + - - +
23C LYS* 3.7 9.2 - - - +
24C SER* 3.0 30.0 + - - +
161C TYR* 5.5 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN 4.6 0.2 + - - -
19C PHE 3.2 0.6 - - - -
20C ALA* 1.3 78.4 - - - +
22C ILE* 1.3 63.4 + - - +
24C SER* 3.3 6.0 + - - -
25C TYR* 2.9 23.4 + - - +
160C LEU 4.6 2.0 - - - -
161C TYR* 4.3 25.6 - - - -
166C ASN* 5.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 4.4 10.8 - - - -
19C PHE* 3.0 35.0 + - + +
21C GLY* 1.3 74.6 - - - +
23C LYS* 1.3 64.6 + - - +
25C TYR* 3.1 9.2 + - + +
26C LEU* 2.9 41.7 + - + +
74C VAL* 4.6 3.8 - - + -
102C LEU* 3.7 27.6 - - + -
159C LEU 4.8 0.7 - - - +
160C LEU* 3.8 28.6 + - + +
166C ASN* 4.0 15.0 - - - +
169C ILE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 2.9 36.4 - - + +
16C SER 5.3 5.6 - - - -
19C PHE 2.8 20.6 + - - +
20C ALA* 3.7 7.6 - - - +
22C ILE* 1.3 74.0 - - - +
24C SER* 1.3 56.8 + - - +
25C TYR 3.2 0.2 + - - -
26C LEU* 3.2 3.0 + - - -
27C VAL* 2.9 33.3 + - - +
33C ARG* 3.9 27.6 - - + +
36C LEU* 2.9 48.9 + - + +
37C TYR 4.5 2.4 - - - -
38C ALA* 4.6 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.0 19.7 + - - +
21C GLY* 3.7 5.8 - - - -
23C LYS* 1.3 76.1 - - - +
25C TYR* 1.3 61.6 + - - +
27C VAL* 3.7 3.4 - - - +
28C SER* 3.1 23.0 + - - -
33C ARG* 3.7 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 2.9 13.8 + - - +
22C ILE* 3.3 11.0 - - + +
24C SER* 1.3 75.6 - - - +
26C LEU* 1.3 85.4 + - + +
28C SER* 2.5 26.7 + - - -
29C GLN* 3.1 40.2 + - + +
163C SER* 5.6 0.7 - - - -
166C ASN* 3.1 62.6 + - + +
167C SER* 3.6 12.5 + - - -
169C ILE* 5.6 0.7 - - + -
170C LYS* 3.5 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 4.7 7.4 - - + -
8C MET* 5.3 3.4 - - - -
22C ILE* 2.9 33.3 + - + +
23C LYS* 3.7 4.9 - - - +
25C TYR* 1.3 93.8 - - + +
27C VAL* 1.3 63.3 + - - +
29C GLN* 2.9 10.6 + - - +
30C GLY 3.2 0.9 + - - -
31C TRP* 3.1 53.4 + - + -
36C LEU* 4.0 24.0 - - + -
74C VAL* 5.3 1.6 - - + -
169C ILE* 4.4 7.9 - - + -
170C LYS* 4.9 2.0 - - - -
173C LEU* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LYS 2.9 21.7 + - - +
24C SER 3.7 5.4 - - - +
26C LEU* 1.3 76.9 - - - +
28C SER* 1.3 61.9 + - - +
29C GLN 3.1 1.0 + - - -
30C GLY* 3.2 10.6 + - - -
31C TRP 3.5 16.0 - - - +
33C ARG* 3.3 55.4 - - + +
36C LEU* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C SER 3.1 9.5 + - - -
25C TYR* 2.5 27.6 + - - -
27C VAL* 1.3 79.9 - - - +
29C GLN* 1.3 72.9 + - - +
30C GLY 3.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C HIS* 4.8 2.4 - - - -
25C TYR* 3.3 47.4 + - + +
26C LEU* 2.9 10.4 + - - +
28C SER* 1.3 95.6 + - - +
30C GLY* 1.3 55.4 + - - +
31C TRP* 3.7 23.5 - - + -
170C LYS* 3.6 24.2 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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