Contacts of the strand formed by residues 16 - 24 (chain K) in PDB entry 6D6Q
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 16 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA 4.8 8.7 - - - +
65E GLU* 5.2 6.4 - - - +
66E MET* 3.5 32.7 + - + +
133E TRP* 4.1 18.6 - - + -
166E PRO* 4.7 4.3 - - + -
168E VAL* 4.7 2.5 - - + -
180E ILE* 5.6 1.8 - - + -
182E LEU* 3.7 29.8 - - + -
8K LEU* 4.1 14.4 - - + -
9K LYS 3.2 13.5 - - - +
10K LYS* 5.0 2.7 - - + +
11K THR* 4.7 2.0 - - - +
15K GLY* 1.3 74.7 - - - -
17K MET* 1.3 73.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY* 4.2 24.7 - - - +
84B GLU* 3.5 35.4 - - + +
63E LYS* 5.9 1.1 - - - +
8K LEU* 3.3 10.8 - - - +
9K LYS* 2.9 67.0 + - + +
11K THR* 3.5 24.4 - - + +
16K VAL* 1.3 78.3 - - - +
18K LYS* 1.3 66.1 + - - +
44O C 3.5 15.5 - - - +
45O C 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY* 5.1 5.9 - - - -
43E SER 3.1 22.9 + - - -
44E ASN* 4.2 18.5 - - - +
45E THR 2.6 30.8 + - - -
46E SER* 4.3 11.3 - - - +
6K THR* 4.7 12.6 - - - +
7K PHE 3.8 7.9 - - - +
8K LEU* 4.3 18.6 - - + +
17K MET* 1.3 85.2 - - - +
19K ILE* 1.3 79.6 + - - +
20K VAL* 4.3 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ASN* 4.8 2.2 - - - -
5K LYS 4.6 0.2 - - - -
6K THR* 3.1 8.1 - - - -
7K PHE* 2.9 54.2 + - + +
9K LYS* 3.5 31.9 - - + +
18K LYS* 1.3 79.1 - - - +
20K VAL* 1.3 69.3 + - - +
21K ARG* 3.5 32.5 - - + +
44O C 5.0 3.1 - - - +
45O C 3.2 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASN* 3.6 23.9 - - - +
128B GLN* 5.1 1.3 + - - +
130B ASP* 3.8 8.0 - - - +
43E SER* 3.4 49.8 - - - +
44E ASN* 3.9 16.8 + - - +
4K SER* 4.3 20.2 - - - -
5K LYS 3.7 3.4 - - - -
6K THR* 3.6 24.2 - - + -
18K LYS* 4.3 7.4 - - - -
19K ILE* 1.3 80.7 - - - +
21K ARG* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.3 22.2 - - - +
13B VAL* 4.4 17.7 - - - +
14B ASP* 5.0 5.4 - - - +
44B ASN* 4.5 1.3 - - - -
130B ASP* 5.0 3.4 - - - +
175B VAL* 4.4 15.7 - - + +
4K SER* 3.3 6.6 - - - -
5K LYS* 2.9 62.7 + - - +
7K PHE* 3.5 20.5 - - + -
19K ILE* 3.5 19.5 - - + +
20K VAL* 1.3 75.7 - - - +
22K GLU* 1.3 68.7 + - - +
45O C 2.4 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 4.9 1.6 - - - +
14B ASP* 3.4 29.7 + - - +
43B GLY* 4.8 6.0 - - - +
44B ASN* 2.3 51.6 + - - +
130B ASP* 5.5 0.2 + - - -
2K LEU* 3.0 37.9 - - + +
3K LYS 3.5 7.0 - - - +
4K SER* 4.2 12.8 + - - -
5K LYS* 4.8 4.4 - - - -
21K ARG* 1.3 81.1 - - - +
23K HIS* 1.3 63.5 + - - +
24K TYR* 4.3 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL 4.6 1.6 + - - -
14B ASP 3.4 2.0 - - - -
2K LEU* 3.7 2.4 - - - -
3K LYS* 2.8 46.7 + - + +
5K LYS* 4.8 23.6 - - + -
22K GLU* 1.3 79.4 + - - +
24K TYR* 1.3 62.2 + - - +
25K LEU* 3.8 12.8 + - + -
126K GLU* 2.6 43.5 + - + -
127K HIS* 3.2 33.2 + + - -
132K TYR* 3.4 29.6 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 2.6 36.4 + - + +
15B GLY 3.3 23.3 - - - +
16B ARG* 3.3 31.4 + - + -
21B LEU 5.5 0.9 - - - -
22B ARG* 2.7 37.9 - - + +
23B LYS* 4.1 11.6 + - + +
43B GLY* 5.1 1.9 - - - -
1K MET 3.8 9.9 - - - +
2K LEU* 3.2 32.9 - - + +
22K GLU* 4.3 14.3 - - + +
23K HIS* 1.3 71.2 - - - +
25K LEU* 1.3 61.4 + - - +
26K ARG* 3.4 8.3 + - + -
127K HIS* 3.3 24.6 + - - +
----------------------------------------------------------
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