Contacts of the strand formed by residues 40 - 46 (chain A) in PDB entry 3IKK
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 VAL 40 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.6 5.4 - - + -
8A LEU* 4.1 16.6 - - + -
34A ASN* 3.2 33.4 - - - +
38A ARG 3.6 4.5 - - - +
39A ASN* 1.3 78.6 - - - +
41A CYS* 1.3 76.5 + - - +
42A PHE* 3.5 1.7 + - - +
60A ILE* 4.3 1.1 - - - -
61A ILE* 3.0 35.2 + - - +
92A SER* 3.8 12.6 - - - -
93A MET 3.5 19.5 - - - +
94A PHE* 3.9 21.1 - - + +
115A MET* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN 4.1 0.2 - - - -
40A VAL* 1.3 76.0 - - - +
42A PHE* 1.3 60.0 + - - +
59A GLY 3.2 6.7 - - - -
60A ILE* 3.4 24.0 - - - -
92A SER* 3.2 5.0 - - - -
93A MET* 2.7 40.9 + - + +
95A ALA* 3.5 25.3 - - - +
96A PRO* 5.3 2.5 - - - -
101A ASP 5.1 2.0 - - - -
102A MET* 3.9 22.7 - - + -
105A VAL* 5.9 2.0 - - - -
106A TRP* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.5 17.7 - - + -
32A LEU* 3.8 18.6 - - + -
40A VAL 4.4 2.2 - - - +
41A CYS* 1.3 75.2 - - - +
43A LYS* 1.3 63.0 + - - +
44A VAL* 3.1 35.7 - - + -
56A PRO* 3.9 12.1 - - + -
58A SER* 3.0 24.7 - - - -
59A GLY* 2.6 67.9 + - - +
60A ILE 4.2 0.4 - - - -
61A ILE* 3.8 15.7 - - + -
67A ILE* 3.5 31.2 - - + -
69A VAL* 4.4 2.0 - - + -
90A VAL* 4.7 2.0 - - + -
91A GLN 3.1 10.5 - - - +
102A MET* 4.8 0.2 - - - +
106A TRP* 3.6 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 1.3 77.5 - - - +
44A VAL* 1.3 62.6 + - - +
45A LYS* 3.0 42.0 - - + +
57A ASN* 3.3 8.1 + - - +
58A SER* 4.1 17.4 - - - -
89A MET 3.7 0.5 - - - +
90A VAL* 3.4 8.0 - - - +
91A GLN* 2.7 32.4 + - + +
102A MET* 5.9 0.4 - - - +
106A TRP* 3.8 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.4 18.4 - - + -
32A LEU* 5.1 2.2 - - + -
42A PHE* 3.1 34.5 - - + -
43A LYS* 1.3 71.6 - - - +
45A LYS* 1.3 66.5 + - - +
46A THR 4.4 0.2 + - - -
54A VAL* 3.4 34.5 - - + +
56A PRO 3.3 11.7 - - - +
57A ASN* 2.5 27.6 + - - +
69A VAL* 4.1 12.1 - - + -
71A VAL* 5.1 4.5 - - + -
88A PHE* 5.7 4.0 - - + -
89A MET 3.4 8.7 - - - +
90A VAL* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.0 50.4 - - + +
44A VAL* 1.3 80.2 - - - +
46A THR* 1.3 64.0 + - - +
54A VAL* 5.4 0.8 - - - +
88A PHE* 3.5 5.9 - - - +
89A MET* 2.8 66.4 + - + +
91A GLN* 3.1 36.3 + - + +
106A TRP* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 1.3 80.7 - - - +
47A THR* 1.3 66.8 + - - +
48A ALA 3.9 1.8 - - - +
49A PRO* 3.7 38.0 - - + +
52A TYR* 3.4 37.4 - - + +
54A VAL* 4.9 11.9 - - + -
87A LYS 3.7 6.0 + - - -
88A PHE* 3.8 13.1 - - - +
89A MET* 5.4 5.3 - - - +
----------------------------------------------------------
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