Contacts of the strand formed by residues 18 - 24 (chain B) in PDB entry 2ZHX
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 ILE 18 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 5.0 7.0 - - + +
72A THR* 3.8 11.4 - - - +
4B LEU* 3.4 34.1 - - + -
5B SER* 4.5 16.1 - - - +
8B ILE* 4.1 24.5 - - + -
16B LEU 3.9 1.4 + - - +
17B VAL* 1.3 82.6 - - - +
19B GLN* 1.3 62.6 + - - +
20B GLU 3.8 21.1 - - - +
21B SER* 4.2 7.4 - - - +
44B HIS* 3.6 24.2 - - + -
45B THR 4.1 1.1 - - - +
46B ALA* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.4 18.4 - - - -
71A PRO* 4.0 3.6 - - - +
72A THR* 3.9 17.2 - - - +
75A HIS* 2.9 34.1 + - + -
87A VAL* 4.4 3.2 - - - +
89A PRO* 2.3 41.9 + - - +
90A TRP 3.2 14.2 - - - +
91A PRO* 3.9 19.9 - - + +
92A ARG 4.8 1.6 + - - +
17B VAL* 3.6 19.0 - - + +
18B ILE* 1.3 74.8 - - - +
20B GLU* 1.3 62.8 + - + +
45B THR 3.2 11.4 + - - +
46B ALA* 5.1 3.1 - - - -
47B TYR* 4.9 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.2 15.0 - - + -
71A PRO* 4.4 7.2 - - - +
91A PRO* 3.8 5.1 - - + +
92A ARG 3.5 9.1 + - - +
93A SER* 2.7 52.1 + - - -
193A SER* 3.9 5.9 - - - -
194A PRO* 4.2 0.5 - - - +
18B ILE* 3.6 4.1 - - - +
19B GLN* 1.3 82.9 - - + +
21B SER* 1.3 62.9 + - - +
22B ILE* 3.3 20.2 - - + +
43B VAL 3.4 0.5 - - - +
44B HIS* 3.1 3.8 - - - -
45B THR* 2.9 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 4.0 5.2 - - - +
68A ASP* 4.6 10.6 - - - +
71A PRO* 4.6 8.6 - - - +
137A PRO* 3.5 31.1 - - - +
18B ILE* 4.2 4.9 - - - +
20B GLU* 1.3 75.4 + - - +
22B ILE* 1.3 66.0 + - - +
23B LEU 3.9 0.7 + - - -
42B LEU* 3.8 13.1 - - - +
43B VAL 3.6 4.7 - - - -
44B HIS* 2.7 35.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 3.4 17.7 - - + +
70A TYR* 5.7 5.2 - - + -
81A PHE* 5.3 4.3 - - + -
93A SER* 4.0 5.6 - - - +
191A HIS* 3.3 59.9 - - + +
193A SER* 4.1 8.1 - - - -
20B GLU* 3.3 30.3 - - + +
21B SER* 1.3 78.7 - - - +
23B LEU* 1.3 65.4 + - - +
24B MET* 4.5 5.2 - - + -
42B LEU* 4.0 1.3 - - - -
43B VAL* 2.6 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 2.8 34.5 + - - +
141A ARG* 3.3 33.7 - - - +
169A GLY* 6.1 1.2 - - - -
171A ASP* 4.4 23.0 + - + +
21B SER 3.9 0.4 + - - -
22B ILE* 1.3 70.5 - - - +
24B MET* 1.3 67.5 + - - +
25B LEU* 5.8 2.9 - - + -
28B GLU* 4.6 1.4 - - - +
40B ASP* 3.7 31.4 - - + +
41B ILE 3.2 20.6 - - - +
42B LEU* 3.8 15.0 - - + -
61B ASP* 3.9 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY* 5.2 0.7 - - - -
171A ASP 6.0 0.7 - - - +
191A HIS* 3.8 18.2 - - + +
193A SER* 5.2 3.1 - - - -
195A LEU* 4.2 16.4 - - - -
196A SER* 3.5 31.6 - - - +
22B ILE* 4.2 6.1 - - + +
23B LEU* 1.3 80.3 - - - +
25B LEU* 1.3 67.8 + - - +
28B GLU* 3.3 48.2 - - + +
29B VAL* 4.2 10.8 - - + -
40B ASP* 3.4 5.3 - - - +
41B ILE* 2.7 35.5 + - - +
43B VAL* 3.6 28.9 - - + -
----------------------------------------------------------
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