Contacts of the strand formed by residues 14 - 23 (chain F) in PDB entry 2PY2
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 ARG 14 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F CYS* 4.5 0.2 - - - -
9F LYS 3.8 0.2 - - - +
10F MET* 3.5 4.9 - - - +
11F PHE 2.9 30.1 + - - +
12F ASN 4.3 7.4 - - - +
13F GLY* 1.3 84.5 - - - +
15F CYS* 1.3 65.5 + - - +
16F PHE* 3.6 19.8 - - + -
40F ALA* 4.2 0.2 - - - +
41F SER* 2.9 50.0 + - - +
43F HIS* 3.8 7.7 - - - -
47F GLU* 2.5 36.6 + - - -
79F ASP* 3.3 9.9 + - - -
81F THR* 5.8 2.0 - - - +
126F ALA* 3.6 20.2 - - - +
127F LYS* 3.3 14.1 - - - +
128F PRO* 4.6 5.2 - - + -
129F LEU* 4.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F CYS* 2.0 53.6 - - + -
5F PRO* 4.1 6.7 - - + -
8F TRP* 3.5 19.5 - - + -
9F LYS 3.3 4.7 - - - -
14F ARG* 1.3 75.8 - - - +
16F PHE* 1.3 61.2 + - - +
126F ALA* 3.1 7.1 - - - +
127F LYS* 2.7 38.9 + - + +
128F PRO 4.6 1.8 - - - -
129F LEU* 3.8 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASP 4.4 0.9 - - - +
8F TRP* 3.4 7.0 - - - -
9F LYS* 2.7 45.1 + - - +
11F PHE* 3.8 20.2 - - + -
14F ARG* 3.6 34.8 - - + -
15F CYS* 1.3 76.3 - - - +
17F LEU* 1.3 61.2 + - - +
40F ALA* 4.0 15.5 - - + -
41F SER 4.5 2.0 - - - -
47F GLU* 3.3 28.9 - - + -
50F PHE* 3.7 16.2 - + + -
51F VAL* 4.0 22.2 - - + -
54F LEU* 3.5 21.1 - - + +
124F ILE* 4.2 3.8 - - + -
125F CYS 3.2 6.7 - - - +
126F ALA* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASP* 4.3 21.1 - - + +
8F TRP* 3.5 45.5 - - + +
16F PHE* 1.3 76.6 - - - +
18F PHE* 1.3 79.9 + - - +
19F ASN* 3.7 13.6 + - + +
35F GLU* 4.4 13.9 - - - +
54F LEU* 4.7 5.6 - - - -
124F ILE* 3.5 4.1 - - - +
125F CYS* 2.8 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 1.3 82.4 - - - +
19F ASN* 1.3 58.1 + - - +
20F PRO* 3.2 33.7 - - + +
54F LEU* 3.4 34.7 - - + +
55F THR* 3.9 13.9 - - + -
56F SER* 5.9 1.1 - - - -
60F ILE* 3.8 30.3 - - + -
62F SER* 3.3 23.1 - - - -
122F SER* 3.6 26.2 - - - -
123F SER 3.6 6.7 - - - -
124F ILE* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 3.7 14.2 - - + +
18F PHE* 1.3 72.3 - - - +
20F PRO* 1.3 64.8 - - - +
21F LEU* 3.0 26.0 + - - +
23F LEU* 3.8 21.6 - - - +
28F ALA 5.3 0.2 + - - -
31F SER* 3.5 25.4 + - - -
122F SER* 3.4 3.8 - - - -
123F SER* 2.8 47.8 + - - +
125F CYS* 4.9 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F PHE* 3.2 31.9 - - + +
19F ASN* 1.3 84.6 - - - +
21F LEU* 1.3 60.1 + - - +
22F GLN* 2.9 26.2 + - - +
60F ILE* 6.1 1.3 - - + -
122F SER* 3.3 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 3.0 23.7 + - - +
20F PRO* 1.3 81.6 - - - +
22F GLN* 1.3 64.3 + - - +
23F LEU* 3.3 33.4 + - + +
31F SER* 5.7 1.8 - - - +
121F HIS 3.3 12.5 - - - +
122F SER* 3.6 4.2 - - - -
123F SER* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PRO 2.9 15.5 + - - +
21F LEU* 1.3 72.4 - - - +
23F LEU* 1.3 68.3 + - - +
60F ILE* 5.6 0.6 - - - +
120F LEU* 3.6 27.5 - - + +
121F HIS* 3.5 18.8 + - - -
122F SER* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 3.8 25.6 - - - +
21F LEU* 3.9 30.3 - - + +
22F GLN* 1.3 82.6 - - - +
24F HIS* 1.3 68.9 + - - +
27F ASP* 3.8 36.6 - - + +
28F ALA* 3.9 11.0 - - + +
31F SER* 4.3 5.6 - - - -
63F TRP* 3.0 10.0 + - - -
120F LEU* 3.6 9.4 - - - -
121F HIS 3.0 27.2 + - - +
123F SER* 5.4 0.2 - - - +
----------------------------------------------------------
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