Contacts of the strand formed by residues 37 - 46 (chain A) in PDB entry 6NQN
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 LYS 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.2 1.4 - - - -
32A LYS* 2.7 39.5 + - + +
35A GLU* 3.7 26.7 + - + +
36A GLY* 1.3 82.6 - - - +
38A GLN* 1.3 61.5 + - - +
68A PHE* 3.7 3.7 - - - -
211A GLU 3.4 5.4 - - - +
212A HIS* 3.7 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.6 21.1 - - + +
30A LEU 3.4 13.0 - - - +
31A GLY* 3.8 2.7 - - - -
37A LYS* 1.3 77.2 - - - +
39A SER* 1.3 64.5 + - - +
40A MET* 3.9 4.7 - - - +
61A PHE 4.6 0.5 - - - +
63A KZ4 3.7 30.1 - - - +
65A ASN* 4.3 6.4 + - - +
68A PHE* 3.7 34.4 - - + +
116A TYR* 4.4 2.4 + - - -
210A HIS* 3.4 5.2 + - - +
211A GLU* 2.6 65.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.8 1.4 - - - +
29A GLY* 3.2 1.7 - - - -
30A LEU* 2.9 48.0 + - - +
38A GLN* 1.3 76.4 - - - +
40A MET* 1.3 65.5 + - - +
63A KZ4 6.1 0.2 - - - -
208A ASN* 4.9 3.6 + - - -
209A LEU 3.1 8.5 - - - -
210A HIS* 3.4 35.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.1 17.0 - - + -
12A LEU* 3.7 27.1 - - + -
27A GLY* 5.5 0.7 - - - -
28A VAL 3.3 15.5 - - - +
29A GLY* 3.7 4.3 - - - -
38A GLN* 3.9 11.7 - - - +
39A SER* 1.3 77.4 - - - +
41A ASP* 1.3 65.7 + - - +
42A LEU* 3.8 15.0 - - + -
61A PHE* 3.7 36.1 - - - +
63A KZ4 3.8 14.8 - - - -
116A TYR* 4.8 0.2 - - + -
207A VAL 3.7 0.9 - - - +
208A ASN* 3.4 5.8 + - - +
209A LEU* 2.9 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU 4.1 0.2 - - - +
27A GLY* 3.2 2.8 - - - -
28A VAL* 2.8 45.6 + - + +
40A MET* 1.3 75.7 - - - +
42A LEU* 1.3 61.6 + - - +
43A LYS* 5.2 9.5 - - - +
207A VAL 3.4 3.4 - - - +
208A ASN* 3.3 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 3.4 - - + -
25A ILE* 4.1 4.0 - - + -
26A GLU 3.4 3.8 - - - +
27A GLY* 3.9 15.9 - - - -
40A MET* 3.8 16.2 - - + -
41A ASP* 1.3 74.9 - - - +
43A LYS* 1.3 64.7 + - - +
54A TYR* 3.4 21.1 - - + +
61A PHE* 3.6 53.8 - - + -
205A SER 3.4 1.1 - - - +
206A ASN* 3.4 7.1 - - - +
207A VAL* 2.8 40.4 + - + +
209A LEU* 3.8 30.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
25A ILE* 3.4 4.4 - - - +
26A GLU 2.8 35.8 + - - +
41A ASP* 5.2 8.9 - - + +
42A LEU* 1.3 80.1 - - - +
44A VAL* 1.3 65.3 + - - +
45A LYS* 3.4 34.5 + - + +
205A SER 3.2 5.8 - - - +
206A ASN* 3.2 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
24A ALA 3.7 4.9 - - - +
25A ILE* 3.8 12.3 - - + -
43A LYS* 1.3 72.9 - - - +
45A LYS* 1.3 64.1 + - - +
46A GLU 3.5 21.8 - - - +
48A GLY* 3.9 24.0 - - - +
50A LEU* 3.7 31.4 - - + +
54A TYR* 4.4 2.2 - - + -
203A ASP 5.6 0.4 - - - +
204A TYR 3.7 22.2 - - - +
205A SER* 3.0 21.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
13A ARG* 4.6 8.5 - - - +
24A ALA 2.8 10.5 + - - +
25A ILE 4.6 0.2 - - - -
26A GLU* 3.7 48.5 - - + +
43A LYS* 3.5 41.9 - - - +
44A VAL* 1.3 79.1 - - - +
46A GLU* 1.3 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 3.1 24.4 + - - -
15A GLU* 5.9 0.3 - - - -
22A PRO 6.0 0.2 - - - -
23A PHE* 3.4 8.9 - - - +
24A ALA* 3.1 46.8 + - + +
44A VAL* 3.5 4.7 - - - +
45A LYS* 1.3 84.9 - - + +
47A GLY* 1.3 64.7 + - - +
48A GLY 3.3 4.4 + - - +
----------------------------------------------------------
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