Contacts of the strand formed by residues 56 - 60 (chain K) in PDB entry 3J7Y
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 HIS 56 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ARG* 3.8 39.6 + - + +
17K ILE 2.8 7.8 + - - +
18K TRP* 3.5 55.1 + + + -
19K TYR* 2.8 31.8 + - - -
55K ASP* 1.3 73.7 - - - +
57K VAL* 1.3 61.2 + - - +
58K VAL 4.1 0.2 - - - -
124K ARG* 3.5 26.7 + - + +
126K HIS* 3.5 6.2 + - + -
117a PHE* 3.5 40.8 - + + -
265c THR* 4.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K TYR* 3.8 7.6 - - + +
21K LEU* 3.8 19.3 - - + -
35K ALA* 3.7 20.9 - - + +
38K ARG* 3.5 32.8 - - + -
39K LEU* 4.1 14.4 - - + +
55K ASP 4.0 0.8 + - - +
56K HIS* 1.3 76.4 - - - +
58K VAL* 1.3 64.6 + - - +
59K ILE* 3.7 22.9 - - + -
124K ARG 3.2 8.3 + - - +
125K LEU* 3.5 11.0 - - + +
126K HIS* 2.8 26.5 + - - -
145K LEU* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K TRP* 3.9 14.6 - - + -
19K TYR 2.8 14.4 + - - +
20K LEU* 3.4 16.8 - - + -
21K LEU* 2.8 30.8 + - - +
57K VAL* 1.3 76.3 - - - +
59K ILE* 1.3 60.5 + - - +
126K HIS* 3.4 10.3 - - + -
128K PHE* 3.6 29.6 - - + -
133K ILE* 4.2 7.9 - - + -
137K ILE* 3.4 26.9 - - + -
141K LEU* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 3.3 21.8 - - + +
23K GLY 4.9 0.2 - - - +
31K LEU* 4.3 21.3 - - + -
35K ALA* 4.0 15.3 - - + -
57K VAL* 3.7 11.4 - - + -
58K VAL* 1.3 80.8 - - - +
60K MET* 1.3 65.4 + - - +
62K THR* 4.0 18.8 - - + -
104K VAL* 4.1 5.4 - - + -
108K ILE* 3.6 31.6 - - + -
125K LEU* 4.0 4.5 - - + -
126K HIS 2.8 8.2 + - - +
127K LEU* 3.6 18.8 - - + -
128K PHE* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 4.0 8.7 - - + -
21K LEU 2.8 19.4 + - - +
22K ASP* 3.4 22.2 - - + +
23K GLY* 2.8 27.7 + - - -
59K ILE* 1.3 77.6 - - - +
61K ASN* 1.3 62.1 + - - +
62K THR* 3.3 4.2 + - - +
128K PHE* 3.5 6.3 - - + -
130K ASP 3.7 11.0 - - - +
131K GLU* 3.2 37.5 - - - +
133K ILE* 3.5 38.1 - - + -
146b ARG* 3.3 37.2 - - + +
----------------------------------------------------------
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