Contacts of the strand formed by residues 42 - 52 (chain A) in PDB entry 1KK8
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 GLY 42 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.7 2.3 - - - +
38A ASP 2.9 29.2 + - - +
39A GLU 4.7 0.4 - - - -
40A LYS 3.7 0.4 - - - -
41A GLU* 1.3 73.4 - - - +
43A PHE* 1.3 73.8 - - - -
100A LEU* 4.7 0.7 - - - -
684A ALA* 3.4 16.8 - - - +
685A GLU* 5.1 5.7 - - - +
688A LEU* 4.2 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 4.0 27.7 - - + -
36A VAL 3.3 18.8 - - - -
37A PRO* 4.1 20.9 - - + -
38A ASP* 3.8 4.3 - - - -
41A GLU* 2.8 19.4 + - - +
42A GLY* 1.3 78.6 - - - +
44A ALA* 1.3 60.2 + - - +
73A ASP 4.8 1.1 - - - -
75A GLN* 3.0 37.7 - - + -
96A GLU* 4.3 6.5 - - + -
97A ALA* 3.6 33.2 - - + +
100A LEU* 4.1 14.6 - - + +
104A ARG* 4.6 4.7 + - - -
688A LEU* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 3.5 7.0 - - - -
36A VAL* 2.8 34.9 + - + +
38A ASP* 3.5 27.4 - - + +
41A GLU* 5.8 0.7 - - + -
43A PHE* 1.3 74.1 - - - +
45A SER* 1.3 64.8 + - - +
46A ALA 3.4 1.6 + - - -
60A ILE* 4.3 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 5.5 1.7 + - - -
34A CYS 3.9 1.1 - - - -
35A TRP* 3.6 22.5 - - - -
44A ALA* 1.3 71.9 - - - +
46A ALA* 1.3 62.5 + - - +
60A ILE* 3.9 5.2 - - - +
61A VAL* 3.0 43.3 + - - +
62A ALA 4.6 1.0 + - - -
77A MET* 3.9 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN* 3.3 8.0 - - - +
34A CYS* 2.9 39.6 + - - +
36A VAL* 4.1 19.3 - - + -
44A ALA 3.4 0.2 + - - -
45A SER* 1.3 77.7 + - - +
47A GLU* 1.3 66.7 + - - +
58A VAL* 3.9 24.0 - - + -
59A LYS 3.4 13.5 - - - +
60A ILE* 4.5 2.7 - - + -
61A VAL* 4.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA 5.8 0.2 - - - +
32A LYS* 2.7 40.8 + - + +
33A ASN* 3.3 24.0 - - - +
46A ALA* 1.3 76.6 - - - +
48A ILE* 1.3 64.7 + - - +
49A GLN* 3.1 10.7 - - - +
58A VAL* 4.1 2.7 - - - -
59A LYS* 2.8 55.4 + - + +
61A VAL* 3.3 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS 3.8 20.2 - - - +
32A LYS* 2.9 34.9 + - - +
34A CYS* 3.9 19.1 - - + -
46A ALA 4.3 0.2 - - - -
47A GLU* 1.3 69.7 - - - +
49A GLN* 1.3 65.8 + - - +
50A SER 3.9 5.2 - - - +
56A ILE* 3.8 26.7 - - + -
57A THR 3.7 4.5 - - - -
58A VAL* 3.8 9.6 - - + -
74A ILE* 4.7 10.8 - - + -
95C ARG* 3.7 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 5.7 1.4 - - - +
47A GLU* 3.1 19.8 + - - +
48A ILE* 1.3 79.1 - - - +
50A SER* 1.3 63.2 + - - +
57A THR* 2.6 30.6 + - + +
58A VAL 4.1 3.1 - - - +
59A LYS* 3.7 37.5 - - + +
66A THR* 5.3 4.3 - - - +
95C ARG* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.7 0.5 - - - +
49A GLN* 1.3 81.7 - - - +
51A SER* 1.3 62.6 + - - +
56A ILE* 3.3 10.0 - - - +
57A THR* 3.0 38.7 + - - +
95C ARG* 3.3 14.4 - - - +
102C SER* 6.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 1.3 79.5 - - - +
52A LYS* 1.3 62.9 + - - +
53A GLY 3.6 5.2 + - - -
55A GLU 3.9 4.9 - - - -
56A ILE* 3.2 17.8 - - - +
57A THR 4.9 0.2 - - - +
71A LYS* 5.8 0.2 - - - +
93C PHE* 5.0 2.0 + - - -
95C ARG* 2.9 35.7 + - - +
102C SER* 4.4 5.4 + - - -
104C ALA* 5.9 0.9 - - - +
105C GLU* 3.1 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER* 1.3 74.3 + - - +
53A GLY* 1.3 62.2 + - - +
54A ASP 3.4 0.9 + - - -
55A GLU* 2.9 60.7 + - - +
104C ALA* 4.9 10.8 - - + +
105C GLU* 3.0 6.1 - - - -
108C HIS* 3.7 45.3 + - + +
----------------------------------------------------------
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