Contacts of the strand formed by residues 31 - 39 (chain K) in PDB entry 1KQ2
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 GLN 31 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K THR* 3.9 19.3 - - + +
24K VAL 3.2 16.2 - - - +
25K PHE* 3.4 27.2 - - + -
26K PHE* 3.9 2.9 - - - -
29K GLY 4.7 6.9 - - - +
30K PHE* 1.3 97.3 - - - +
32K MET* 1.3 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K VAL 3.8 1.0 - - - +
23K THR* 3.7 4.0 - - - +
24K VAL* 2.9 32.7 + - + +
26K PHE* 3.3 20.8 - - + -
30K PHE* 3.8 19.3 - - + -
31K GLN* 1.3 80.9 - - - +
33K LYS* 1.3 61.8 + - - +
34K GLY 4.0 0.2 - - - -
46K LEU* 4.0 12.6 - - + -
48K SER* 4.6 5.8 - - - +
49K GLN* 5.8 1.8 - - - +
53K HIS* 3.8 38.6 - - + -
55K ILE* 3.2 38.8 - - + -
62M THR* 4.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K GLU* 3.2 39.6 - - + +
22K VAL 3.5 5.4 - - - +
23K THR* 4.2 17.7 - - + +
32K MET* 1.3 73.1 - - - +
34K GLY* 1.3 58.9 + - - +
46K LEU* 4.5 0.4 - - - -
48K SER* 2.7 25.7 + - - -
49K GLN 4.7 1.2 + - - -
66K GLU* 4.6 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K GLU* 3.5 11.4 - - - -
22K VAL* 2.8 38.0 + - - +
32K MET 4.0 1.2 - - - -
33K LYS* 1.3 78.2 - - - +
35K VAL* 1.3 66.4 + - - -
46K LEU* 3.9 14.9 - - - +
47K ASN 3.3 11.4 - - - -
48K SER* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE 5.2 0.4 - - - +
16K LYS 5.4 0.2 - - - +
19K GLN* 4.1 37.2 - - + +
20K THR 3.9 11.7 - - - +
21K GLU* 4.1 16.8 - - - +
34K GLY* 1.3 78.1 - - - +
36K ILE* 1.3 74.8 + - - +
37K GLU* 3.3 8.5 + - + +
46K LEU* 3.4 4.4 - - - +
47K ASN* 2.7 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K LEU* 3.9 24.9 - - + +
15K PHE* 3.8 36.1 - - + +
16K LYS* 3.3 35.1 - - + +
20K THR 4.5 3.6 + - - -
22K VAL* 4.0 17.3 - - + -
34K GLY 4.2 0.2 + - - -
35K VAL* 1.3 79.6 - - - +
37K GLU* 1.3 62.1 + - - +
38K GLU 4.1 15.0 - - - +
39K TYR* 4.3 10.8 - - + -
44K VAL* 4.3 12.3 - - + -
45K SER 3.6 4.3 - - - +
46K LEU* 4.2 8.7 - - + -
63K TYR* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K LYS* 3.0 34.3 + - - +
35K VAL* 3.3 7.7 + - + +
36K ILE* 1.3 77.1 - - - +
38K GLU* 1.3 69.8 + - + +
45K SER* 3.0 11.3 + - - +
47K ASN* 3.6 28.6 + - + +
52K GLN* 2.5 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K LYS* 4.5 8.5 - - - +
36K ILE* 4.1 4.3 - - - +
37K GLU* 1.3 85.9 - - + +
39K TYR* 1.3 76.4 + - - +
44K VAL* 3.7 0.3 - - - -
45K SER* 2.9 38.9 + - - +
7M ILE* 3.2 32.9 - - + +
10M LYS* 4.7 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K ASP* 3.2 39.4 + - - +
12K LEU* 3.6 41.1 - - + -
13K GLU* 3.3 25.6 + - - +
16K LYS* 4.3 15.5 - - + -
36K ILE* 4.3 9.0 - - + -
38K GLU* 1.3 86.9 - - - +
40K ASP* 1.3 68.7 + - - +
43K VAL 3.8 15.0 - - - +
44K VAL* 4.0 15.0 - - + +
45K SER 4.5 0.2 - - - +
57K LYS* 5.1 0.4 - - - -
7M ILE* 3.7 13.6 - - - +
----------------------------------------------------------
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