Contacts of the strand formed by residues 5 - 14 (chain A) in PDB entry 2NNA
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 HIS 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.7 1.6 - - - +
4A ASP* 1.3 99.5 + - + +
6A VAL* 1.3 66.9 + - - +
26A PHE* 3.7 26.9 - + + -
27A ASP* 2.7 33.0 - - - +
15B CYS 3.9 0.2 - - - +
16B TYR* 3.5 3.3 - - - -
17B PHE* 2.8 45.3 + - + +
20B GLY 6.4 0.4 - - - -
83B TYR* 4.3 15.4 + + - -
91B LEU* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ILE 5.1 6.1 - - - +
3A ALA* 4.5 11.9 - - + +
5A HIS* 1.3 80.1 - - - +
7A ALA* 1.3 61.6 + - - +
26A PHE* 3.8 1.5 - - - -
27A ASP* 2.7 42.2 + - - +
28A GLY 4.5 1.1 + - - +
14B MET* 3.8 21.3 - - + -
15B CYS 3.4 4.5 - - - +
16B TYR* 3.6 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS 4.3 0.2 - - - -
6A VAL* 1.3 77.9 - - - +
8A SER* 1.3 63.0 + - - +
9A TYR* 3.5 37.0 - - + +
25A GLU 3.3 9.6 - - - +
26A PHE* 3.6 15.0 - - + -
14B MET* 3.2 9.2 - - - +
15B CYS* 2.9 30.9 + - + +
17B PHE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 1.3 72.1 - - - +
9A TYR* 1.3 65.1 + - - +
10A VAL* 3.4 32.0 - - - +
23A SER 4.0 0.2 - - - +
24A HIS* 3.1 9.0 - - - +
25A GLU* 2.8 43.3 + - - +
139A SER* 4.4 3.8 + - - -
12B LYS* 5.4 2.4 - - - +
13B GLY 3.4 7.4 - - - -
14B MET* 3.6 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.5 22.4 - - + +
8A SER* 1.3 74.3 - - - +
9A GLY* 1.3 55.3 + - - +
22A TYR* 3.8 1.2 + - - -
24A HIS* 3.4 33.5 + + + -
25A GLU 4.4 3.1 - - - -
26A PHE* 3.4 9.2 - - - -
31A GLU* 3.7 11.2 - - - -
13B GLY 2.8 10.7 + - - -
15B CYS* 3.6 27.8 - - - -
17B PHE* 4.4 8.6 - + - -
78B VAL* 3.8 15.0 - - + -
82B ASN* 3.3 41.6 + - + +
86B GLU* 2.7 43.4 + - - +
3C GLU* 4.6 1.6 - - - -
4C GLY 4.2 0.2 - - - +
5C SER* 3.9 0.2 - - - -
6C PHE* 3.2 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.0 6.0 + - - -
9A TYR* 1.3 79.2 - - - +
10A VAL* 1.3 53.4 + - - +
11A ASN* 2.8 19.5 + - - +
22A TYR* 3.8 11.4 - - - -
23A SER 4.1 2.2 - - - -
24A HIS* 3.5 3.2 - - - -
11B PHE 2.7 25.3 - - - +
12B LYS* 3.2 0.9 - - - -
13B GLY* 3.1 19.6 + - - +
6C PHE* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.4 28.7 - - - +
9A GLY* 1.3 70.4 - - - +
11A ASN* 1.3 60.2 + - - +
12A LEU* 5.6 1.8 - - + -
21A GLN* 3.6 13.8 - - - +
22A TYR* 3.6 4.9 - - - -
23A SER* 3.0 44.6 + - - +
25A GLU* 3.6 27.8 - - + +
137A PHE 5.1 0.9 - - - +
139A SER* 4.0 20.0 - - - +
145A PHE* 4.8 11.4 - - + -
10B GLN* 5.9 0.2 - - - +
11B PHE 4.0 1.3 - - - -
12B LYS* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 2.8 43.0 + - - +
10A VAL* 1.3 74.0 - - - +
12A LEU* 1.3 61.4 + - - +
21A GLN 3.6 3.8 - - - -
22A TYR* 3.1 18.8 - - - -
62A ASN* 3.0 32.7 + - - +
63A ILE* 4.5 3.5 - - + +
66A LEU* 3.5 20.0 - - + -
10B GLN* 3.3 7.4 - - - +
11B PHE* 2.8 52.6 + - + +
12B LYS* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.4 2.0 - - + +
11A ASN* 1.3 75.8 - - - +
13A TYR* 1.3 75.0 + - - +
14A GLN* 4.7 7.6 - - + +
19A SER 5.1 0.4 - - - +
20A GLY* 2.9 7.2 - - - -
21A GLN* 2.8 57.1 + - + +
63A ILE* 3.7 6.2 - - - +
66A LEU* 4.0 2.4 - - - +
115A PRO* 3.7 31.6 - - + +
137A PHE* 4.9 8.5 - - + -
145A PHE* 4.2 18.8 - - + -
8B VAL* 3.6 24.0 - - + -
9B TYR 3.5 11.7 - - - +
10B GLN* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 1.3 77.7 - - - +
14A GLN* 1.3 63.3 + - - +
15A SER* 4.8 1.6 - - - -
18A PRO* 3.3 35.2 - - + +
19A SER 3.4 17.3 - - - -
20A GLY 4.6 0.2 - - - -
63A ILE* 3.8 23.3 - - + -
66A LEU* 3.8 22.0 - - + -
67A LYS* 3.5 54.2 - - + +
70A LEU* 3.6 23.5 - - + +
71A ASN* 5.7 2.0 - - - -
9B TYR* 2.7 40.8 + - + +
----------------------------------------------------------
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