Contacts of the helix formed by residues 21 - 34 (chain A) in PDB entry 3CVW
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 ASN 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 3.5 21.6 + - - -
12A PHE* 3.9 1.4 - - - -
15A GLY 3.6 15.1 + - - -
17A ARG* 3.2 25.1 + - + +
18A LEU 3.7 15.7 + - - +
19A HIS 3.2 2.2 - - - +
20A ASP* 1.3 78.0 - - - +
22A PRO* 1.3 53.3 - - - +
23A ALA* 3.5 12.6 + - - +
24A LEU* 3.1 22.7 + - + +
25A SER* 2.8 38.7 + - - -
108A GLU* 5.0 7.3 - - - +
138A SER* 4.6 5.3 + - - -
175A LEU* 4.7 2.0 - - - +
176A GLY 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP* 3.5 10.5 - - - +
21A ASN* 1.3 86.7 - - - +
23A ALA* 1.3 57.9 + - - +
25A SER* 4.2 1.5 - - - -
26A HIS* 3.1 30.1 + - - +
136A HIS* 3.4 36.9 + - + +
137A CYS 5.4 0.4 - - - +
138A SER* 3.6 24.9 - - - +
175A LEU* 3.7 24.2 - - + -
273A ARG* 4.0 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 3.5 20.9 - - + +
21A ASN* 3.2 6.8 + - - +
22A PRO* 1.3 80.6 - - - +
24A LEU* 1.3 59.5 + - - +
26A HIS* 4.0 0.7 + - - +
27A ILE* 3.6 8.5 + - - +
106A THR* 2.7 25.7 + - - +
107A PHE 4.0 24.5 - - - +
108A GLU* 4.2 3.1 - - + +
136A HIS* 3.5 26.8 - - + -
138A SER* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 3.6 33.2 + - + -
12A PHE* 4.1 13.2 - - + -
17A ARG 3.7 22.2 - - - +
18A LEU* 3.8 28.9 - - + -
21A ASN* 3.1 23.7 + - + +
23A ALA* 1.3 78.7 - - - +
25A SER* 1.3 64.3 + - - +
26A HIS 3.3 0.7 - - - -
27A ILE* 3.2 5.2 + - - +
28A PHE* 3.2 55.0 + - + -
42A PRO* 4.8 3.4 - - + -
75A LEU* 4.8 4.7 - - + -
178A PRO* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN 2.8 23.0 + - - -
22A PRO* 4.2 7.2 - - - -
24A LEU* 1.3 70.3 - - - +
26A HIS* 1.3 52.7 + - - +
28A PHE* 3.8 2.6 - - - +
29A THR* 2.7 47.9 + - - +
175A LEU* 4.4 14.3 - - - +
176A GLY 4.5 6.4 + - - -
177A VAL 5.1 0.2 - - - -
178A PRO* 3.4 30.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 3.1 20.7 + - - +
23A ALA 4.1 4.9 - - - +
24A LEU 3.3 0.2 - - - -
25A SER* 1.3 76.6 - - - +
27A ILE* 1.3 62.7 + - - +
29A THR* 3.4 10.9 + - - -
30A ALA* 3.3 22.0 - - + +
104A MET* 3.6 37.4 - - + +
106A THR* 4.7 4.7 - - + -
132A ARG* 5.3 0.8 + - - -
134A GLU* 4.1 18.2 + - - -
136A HIS* 4.1 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.7 30.1 - - + +
9A VAL 3.5 26.5 - - - +
10A HIS* 4.1 10.3 - - + +
23A ALA 3.6 4.0 - - - +
24A LEU* 3.2 8.6 + - - +
25A SER 3.2 0.2 - - - -
26A HIS* 1.3 78.4 - - - +
28A PHE* 1.3 60.6 + - + +
30A ALA* 3.4 1.3 + - - -
31A ALA* 2.9 28.9 + - - +
40A VAL* 3.9 30.3 - - + -
104A MET* 4.5 10.5 - - + +
106A THR* 3.1 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.2 45.9 + - + +
25A SER 3.2 4.7 + - - +
27A ILE* 1.3 86.3 - - + +
29A THR* 1.3 61.3 - - + +
31A ALA* 4.1 5.0 - - - +
32A ASN* 3.2 31.4 + - - -
40A VAL* 4.2 14.6 - - + -
42A PRO* 4.8 1.1 - - + -
75A LEU* 4.0 20.9 - - + -
78A LEU* 4.1 17.3 - - + -
80A SER* 4.3 7.6 - - - -
178A PRO* 3.7 21.3 - - + -
179A GLU* 3.3 29.4 - - - +
181A LEU* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 2.7 34.0 + - - +
26A HIS* 3.4 13.2 + - - -
28A PHE* 1.3 73.0 - - + +
30A ALA* 1.3 60.0 + - - +
32A ASN* 3.6 1.6 + - - +
33A ALA* 2.9 28.4 + - - +
178A PRO* 6.5 0.9 - - + -
179A GLU* 3.8 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.4 12.6 - - + -
26A HIS* 3.3 22.9 - - + +
27A ILE* 3.4 4.8 + - - +
29A THR* 1.3 79.7 + - - +
31A ALA* 1.3 63.5 + - - +
33A ALA* 3.2 19.7 + - - +
34A ALA* 3.3 9.4 + - - +
38A TYR* 4.8 5.5 - - + -
104A MET* 6.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 12.5 - - + +
27A ILE 2.9 18.0 + - - +
28A PHE 4.1 3.6 - - - +
30A ALA* 1.3 75.4 - - - +
32A ASN* 1.3 59.3 + - - +
34A ALA 3.2 24.4 - - - +
35A PRO* 3.6 4.5 - - - +
36A GLY 4.9 0.3 + - - -
38A TYR* 4.6 10.0 - - + +
40A VAL* 3.8 26.7 - - + -
181A LEU* 4.1 10.3 - - + -
182A LYS 5.5 0.7 - - - +
184A MET* 4.7 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE 3.2 20.2 + - - +
29A THR 4.2 0.9 - - - +
31A ALA* 1.3 76.4 - - - +
33A ALA* 1.3 64.1 + - - +
34A ALA 3.3 0.2 - - - -
35A PRO* 3.4 18.5 - - - +
179A GLU* 3.5 38.8 + - - +
180A LYS 3.9 8.1 + - - -
181A LEU* 3.8 15.9 - - - +
182A LYS* 2.9 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 2.9 17.5 + - - +
30A ALA* 3.2 12.3 + - - +
32A ASN* 1.3 79.0 - - - +
34A ALA* 1.3 58.9 + - + +
35A PRO* 3.4 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.3 5.5 + - - +
31A ALA 3.2 9.4 - - - +
33A ALA* 1.3 79.8 - - + +
35A PRO* 1.3 66.6 - - - +
36A GLY 3.5 0.2 + - - -
37A ARG* 3.4 47.5 + - + +
38A TYR* 4.0 12.9 + - + -
----------------------------------------------------------
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