Contacts of the strand formed by residues 22 - 29 (chain B) in PDB entry 1HDZ
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 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 3.3 0.7 - - - +
12B ALA* 3.2 0.9 - - - -
13B VAL* 2.8 31.7 + - - +
15B TRP* 3.4 20.1 - - - -
20B PRO 3.6 3.2 + - - -
21B PHE* 1.3 73.5 - - - +
23B ILE* 1.3 62.4 + - - +
24B GLU* 3.3 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 4.1 35.0 + - + +
11B ALA 3.6 4.3 - - - +
12B ALA* 4.2 6.3 - - + +
21B PHE 4.5 3.1 - - - +
22B SER* 1.3 72.8 - - - +
24B GLU* 1.3 64.9 + - - +
352B PHE* 4.3 12.8 - - + -
353B GLU* 3.7 40.8 - - + +
355B ILE* 4.1 24.2 - - + -
356B ASN* 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LYS* 3.0 16.3 - - - +
11B ALA 2.8 37.4 + - - +
13B VAL* 4.3 8.7 - - + -
15B TRP* 3.2 28.1 + - - -
22B SER* 3.3 17.6 + - - -
23B ILE* 1.3 79.9 - - - +
25B ASP* 1.3 61.7 + - - +
26B VAL* 3.8 1.1 + - - -
132B CYS* 3.0 18.2 - - - -
133B ARG* 2.8 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 3.9 29.2 - - - +
9B CYS 3.0 9.9 - - - +
10B LYS* 3.1 36.6 + - - +
24B GLU* 1.3 75.2 - - - +
26B VAL* 1.3 64.4 - - - +
27B GLU* 3.8 8.4 - - - +
132B CYS* 4.0 11.4 - - - +
133B ARG 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE 3.6 0.9 - - - +
8B LYS* 3.3 3.7 - - - -
9B CYS* 2.8 39.5 + - - +
11B ALA* 3.5 26.2 - - + -
13B VAL* 4.0 20.2 - - + -
24B GLU 4.6 0.2 - - - +
25B ASP* 1.3 79.9 - - - +
27B GLU* 1.3 65.0 + - - +
28B VAL* 3.9 7.8 + - + -
64B ILE* 4.4 11.0 - - + -
130B PHE* 4.7 1.8 - - + -
131B THR 3.1 20.9 - - - +
132B CYS* 3.5 20.9 - - + -
137B ILE* 4.9 0.9 - - + -
147B SER* 4.1 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.6 25.8 - - + -
7B ILE 3.1 5.8 - - - +
8B LYS* 4.6 20.3 + - + +
25B ASP 3.8 8.3 - - - +
26B VAL* 1.3 82.2 - - - +
28B VAL* 1.3 61.3 + - - +
29B ALA 3.8 0.6 + - - -
129B ARG 3.3 1.2 - - - +
130B PHE* 3.1 6.9 - - - -
131B THR* 2.9 66.0 + - - +
132B CYS* 3.8 5.4 + - - -
133B ARG 4.9 2.3 + - - -
134B GLY 5.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.6 1.4 - - - -
7B ILE* 2.9 26.4 + - + +
9B CYS* 3.8 22.2 - - - -
26B VAL* 4.5 3.1 - - + +
27B GLU* 1.3 70.9 - - - +
29B ALA* 1.3 60.1 + - - +
37B ARG* 2.9 48.6 + - + -
129B ARG 3.3 4.5 - - - -
130B PHE* 3.6 20.9 - - + -
147B SER* 4.3 1.8 - - - +
149B TYR* 3.6 30.3 - - + +
151B VAL* 3.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.1 10.1 - - + -
27B GLU 3.8 1.4 + - - -
28B VAL* 1.3 73.4 - - - +
30B PRO* 1.3 75.9 - - + +
37B ARG* 2.9 10.0 + - - -
128B ARG 5.4 0.4 - - - +
129B ARG* 2.9 39.7 + - + +
151B VAL* 3.4 16.0 - - - +
----------------------------------------------------------
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