Contacts of the helix formed by residues 16 - 26 (chain A) in PDB entry 4ECW
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 CYS 16 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 1.3 76.7 - - - +
17A PHE* 1.3 64.6 + - - +
18A PHE 3.5 1.3 - - - -
19A VAL* 3.1 16.3 + - + -
20A GLN* 3.1 25.5 + - - -
23A GLN* 5.2 1.6 - - - -
49A ALA* 5.0 0.2 - - - -
50A VAL 3.3 26.9 - - - +
51A SER* 4.0 14.1 - - - -
52A TYR* 4.0 18.8 - - + -
55A ARG* 3.6 5.8 - - - +
504P DTP 2.6 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.5 26.5 - - + -
15A ASP 2.9 8.2 + - - -
16A CYS* 1.3 72.0 - - - +
18A PHE* 1.3 85.5 + + - +
20A GLN* 3.1 14.2 + - + +
21A VAL* 3.1 25.7 + - + +
92A TYR 3.7 15.7 - - - -
95A ALA* 3.7 24.0 - - + -
96A SER* 3.7 11.2 - - - -
99A VAL* 4.9 2.0 - - + -
114A ILE* 4.0 15.7 - - + -
115A ASP* 3.5 33.4 - - + +
210A PHE* 4.2 21.8 - + - -
504P DTP 3.1 14.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 1.3 89.6 - + - +
19A VAL* 1.3 61.4 + - - +
21A VAL* 3.4 3.5 + - - +
22A GLU* 3.1 26.9 + - - +
36A VAL* 3.7 9.9 - - + -
48A ILE* 3.6 33.4 - - + -
49A ALA* 3.9 9.2 - - + -
89A LEU* 4.2 15.0 - - + -
92A TYR* 3.4 56.6 - + + -
114A ILE* 4.0 17.9 - - + -
504P DTP 2.8 50.2 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 3.1 13.6 + - + +
17A PHE 3.1 0.2 - - - -
18A PHE* 1.3 75.3 - - - +
20A GLN* 1.3 60.7 + - - +
22A GLU* 3.1 5.3 + - - +
23A GLN* 2.8 50.1 + - + +
34A CYS* 4.1 13.9 - - + +
35A ALA* 4.2 1.1 - - - -
36A VAL* 3.8 14.8 - - + +
49A ALA* 3.6 36.6 - - + +
50A VAL 3.7 4.9 - - - +
51A SER* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 4.5 3.8 - - - +
15A ASP* 2.8 31.2 + - - +
16A CYS* 3.1 15.0 + - - +
17A PHE* 3.1 9.3 + - + +
19A VAL* 1.3 76.3 - - - +
21A VAL* 1.3 58.0 + - - +
23A GLN* 3.8 14.2 - - - +
24A ARG* 2.9 31.2 + - - +
209A GLY 4.1 4.0 - - - +
210A PHE* 3.5 25.1 - - + +
211A GLN* 2.7 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.1 30.5 + - + +
18A PHE 3.6 7.0 - - - +
19A VAL 3.2 0.2 - - - -
20A GLN* 1.3 76.6 - - - +
22A GLU* 1.3 62.2 + - - +
24A ARG* 3.5 8.4 + - - +
25A GLN* 3.3 21.0 + - - +
91A LYS* 3.7 38.6 - - + +
92A TYR* 3.9 17.9 - - + -
95A ALA* 3.6 26.7 - - + -
210A PHE* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE 3.1 13.1 + - - +
19A VAL* 3.1 8.7 + - - +
21A VAL* 1.3 77.5 - - - +
23A GLN* 1.3 55.6 + - - +
25A GLN* 3.3 8.8 + - - +
26A ASN* 2.9 32.1 + - - +
29A LEU* 3.9 8.6 - - + +
34A CYS* 5.7 1.1 - - - -
36A VAL* 3.9 10.5 - - + -
78A ALA* 3.6 33.8 - - + +
79A GLN 4.6 5.6 - - - +
91A LYS* 2.9 31.1 + - - +
92A TYR* 2.6 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 5.2 1.6 - - - -
19A VAL* 2.8 43.8 + - + +
20A GLN* 3.3 18.8 + - - +
22A GLU* 1.3 71.1 - - - +
24A ARG* 1.3 65.5 + - - +
26A ASN 3.3 14.5 - - - +
29A LEU* 3.0 36.4 + - + +
30A ARG* 2.8 37.7 + - + +
31A ASN* 3.9 11.3 - - - +
32A LYS 4.0 12.3 + - - +
34A CYS* 4.2 3.8 - - - +
51A SER* 4.4 4.3 - - - -
53A GLU* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 2.9 17.3 + - - +
21A VAL* 3.7 9.6 + - - +
23A GLN* 1.3 76.4 - - - +
25A GLN* 1.3 63.3 + - - +
27A PRO* 4.4 1.4 - - - +
30A ARG* 2.9 30.0 + - - +
95A ALA* 4.8 4.2 - - - +
98A GLU* 2.9 41.4 + - - -
208A THR* 2.9 32.5 + - - +
209A GLY* 4.8 4.7 - - - -
210A PHE* 3.4 26.8 - - + -
507A GOL 4.3 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL 3.3 9.5 + - - +
22A GLU* 3.3 12.6 + - - +
23A GLN 3.2 0.6 - - - -
24A ARG* 1.3 83.4 - - - +
26A ASN* 1.3 60.2 + - + +
27A PRO* 3.5 7.8 - - - +
91A LYS* 2.9 41.5 + - - +
508A GOL 4.5 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 2.9 13.8 + - - +
23A GLN* 3.3 8.8 - - - +
25A GLN* 1.3 82.6 - - + +
27A PRO* 1.3 58.0 - - - +
28A HIS* 3.1 19.0 + - - +
29A LEU* 2.9 51.9 + - + +
508A GOL 2.9 31.9 + - - +
----------------------------------------------------------
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