Contacts of the strand formed by residues 30 - 35 (chain D) in PDB entry 1EAW
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 30 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TYR* 4.5 12.5 - - + -
22D PHE 3.8 3.8 - - - +
23D TYR* 4.1 2.7 - - - -
24D ASN 4.7 0.2 - - - +
29D LEU* 1.3 87.6 - - - +
31D GLN* 1.3 63.0 + - - +
32D THR* 5.6 0.5 - - - +
48D ALA* 4.8 10.1 - - + +
51D CYS* 2.0 54.5 - - + -
52D MET* 3.4 28.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TYR* 3.2 4.0 - - - -
22D PHE* 2.9 53.7 + - + -
24D ASN* 2.7 40.5 + - + +
27D ALA* 4.5 5.4 - - - +
29D LEU* 4.7 13.6 - - + +
30D CYS* 1.3 76.9 - - - +
32D THR* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 3.9 14.8 - - + +
20D ARG 3.3 5.8 - - - -
21D TYR* 3.3 41.1 - - + -
22D PHE* 3.7 8.1 - - - -
30D CYS 5.6 0.7 - - - +
31D GLN* 1.3 79.0 + - - +
33D PHE* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PRO* 3.7 24.2 - - + -
10D TYR 3.1 27.4 - - - -
11D THR* 4.8 1.6 - - - -
19D ILE* 3.4 9.0 - - - +
20D ARG* 2.9 68.7 + - + -
21D TYR 3.8 4.0 - - - -
22D PHE* 3.4 35.7 - + + -
32D THR* 1.3 75.7 - - - +
34D VAL* 1.3 89.5 + - - +
35D TYR 4.2 2.0 - - - -
43D ASN 4.5 2.7 - - - -
44D ASN* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C HIS* 4.1 22.2 - - + +
148C GLY 5.4 1.6 - - - +
192C GLN* 3.6 35.4 - - + -
11D THR* 2.8 29.3 + - + +
17D ARG* 4.1 13.5 - - + +
18D ILE 3.2 6.3 - - - +
19D ILE* 4.1 18.6 - - + -
33D PHE* 1.3 89.0 - - - +
35D TYR* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP* 4.8 13.1 - - + +
10D TYR* 4.2 5.6 - + - -
11D THR* 3.7 7.6 - - - +
17D ARG* 4.1 2.8 - - - -
18D ILE* 2.7 49.3 + - + +
20D ARG* 3.8 31.2 - - + -
33D PHE* 4.0 4.9 + - + -
34D VAL* 1.3 78.0 - - - +
36D GLY* 1.3 66.5 + - - +
37D GLY* 2.9 31.8 + - - -
38D CYS* 2.9 41.0 - - - -
39D ARG 2.9 1.9 + - - -
40D ALA* 2.9 41.1 + - + +
44D ASN* 3.7 19.7 - - - +
----------------------------------------------------------
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