Contacts of the strand formed by residues 41 - 47 (chain N) 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 41 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N ILE 3.5 1.0 - - - +
23N LEU* 3.2 2.6 - - - -
24N MET* 2.6 44.0 + - - +
25N LEU 5.1 0.8 - - - -
29N VAL* 4.3 12.1 - - + -
37N PRO* 3.6 21.5 - - + +
39N SER 4.0 6.5 - - - +
40N ASP* 1.3 78.6 - - - +
42N LEU* 1.3 69.3 + - - +
43N VAL* 4.3 2.0 - - + +
58N LEU* 3.4 32.5 - - + -
59N THR 3.2 17.5 - - - +
60N SER* 4.7 1.3 - - - +
68N TRP* 3.3 46.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M GLN* 5.2 0.2 - - - +
137M PRO* 5.1 5.8 - - + +
138M ALA* 4.4 20.0 - - + -
141M ARG* 4.7 4.9 - - - +
21N SER* 4.2 16.6 - - - +
22N ILE 3.4 1.6 - - - -
23N LEU* 3.4 32.8 - - + +
41N ILE* 1.3 75.5 - - - +
43N VAL* 1.3 60.0 + - - +
44N HIS* 3.1 32.6 + - + +
58N LEU* 3.3 3.5 - - - -
59N THR* 3.0 27.7 + - - +
60N SER 3.9 12.1 + - - +
61N ASP* 4.0 4.9 - - - +
62N ALA* 3.6 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M SER* 3.9 18.2 - - - +
195M LEU* 3.5 39.3 - - + -
20N GLU 3.7 0.3 - - - +
21N SER* 3.4 2.0 + - - -
22N ILE* 2.6 41.5 + - + +
24N MET* 3.7 19.7 - - + -
29N VAL* 5.6 0.4 - - + -
41N ILE* 4.7 2.9 - - + -
42N LEU* 1.3 70.5 - - - +
44N HIS* 1.3 64.6 + - - +
45N THR* 3.3 16.2 + - - +
56N MET* 4.1 17.3 - - + -
57N LEU 4.0 2.0 - - - -
58N LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M PRO* 4.1 11.8 - - + +
4N LEU* 3.8 31.6 - - + +
8N ILE* 5.9 1.4 - - + +
18N ILE* 4.3 20.4 - - + -
20N GLU 3.4 7.6 - - - +
21N SER* 3.2 23.2 + - - +
42N LEU* 3.1 32.4 + - + +
43N VAL* 1.3 70.5 - - - +
45N THR* 1.3 59.8 + - - +
46N ALA 4.3 0.2 - - - -
55N VAL 3.8 0.5 - - - +
56N MET* 3.1 5.7 - - - -
57N LEU* 2.8 52.9 + - + +
59N THR* 3.2 31.8 + - + +
65N TYR* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M ARG* 3.9 13.6 - - + +
193M SER* 4.0 3.8 + - - -
194M PRO* 3.7 24.2 - - + -
18N ILE* 4.6 1.8 - - - +
19N GLN* 3.2 25.9 + - - +
20N GLU* 3.1 33.8 + - - +
43N VAL* 3.3 17.7 + - - +
44N HIS* 1.3 74.7 + - - +
46N ALA* 1.3 66.1 + - - +
54N ASN* 4.7 2.7 - - + -
55N VAL 3.5 3.1 - - - +
56N MET* 3.5 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M ARG* 4.8 1.1 - - - -
8N ILE* 5.0 6.5 - - + +
16N LEU* 4.3 20.0 - - + -
17N VAL 3.3 29.2 - - - +
18N ILE* 4.0 9.0 - - + +
19N GLN* 4.5 2.7 - - - -
44N HIS 4.3 0.4 - - - -
45N THR* 1.3 78.3 - - - +
47N TYR* 1.3 61.9 + - - +
54N ASN* 3.9 2.9 - - - -
55N VAL* 2.8 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PRO* 4.7 16.0 - - + +
90M TRP 5.5 0.2 - - - +
92M ARG* 3.1 55.9 - - + +
16N LEU* 3.7 13.2 - - - +
17N VAL 4.7 1.8 + - - +
19N GLN* 4.2 15.6 + - - +
46N ALA* 1.3 75.9 - - - +
48N ASP* 1.3 67.3 + - - +
49N GLU* 3.0 53.0 + - + +
52N ASP* 3.2 43.8 + - - +
53N GLU 4.0 4.5 - - - -
54N ASN* 3.5 14.1 - - - -
----------------------------------------------------------
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