Contacts of the strand formed by residues 5 - 10 (chain A) in PDB entry 1YPN
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 3.1 24.8 + - - +
4A ASN* 1.3 84.8 - - + +
6A LEU* 1.3 65.6 + - - +
7A ARG* 4.5 12.9 + - + +
34A LEU* 4.8 0.4 - - - -
35A VAL* 3.4 23.3 - - + +
37A GLU* 3.7 31.9 - - + +
76A ASP* 3.5 9.7 - - - +
211A ARG* 3.1 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN 4.3 0.2 - - - -
5A VAL* 1.3 74.1 - - - +
7A ARG* 1.3 64.8 + - - +
8A ILE* 4.6 3.1 - - + -
27A LEU* 3.4 36.6 - - + -
34A LEU* 4.5 19.4 - - + +
35A VAL 3.0 10.0 + - - +
36A VAL* 3.4 10.2 - - + +
37A GLU 3.0 22.6 + - - +
76A ASP* 3.6 14.8 - - + +
77A ILE* 3.9 18.8 - - + -
211A ARG* 5.2 2.7 - - - +
212A THR* 3.7 36.3 - - + +
215A LEU* 4.7 11.7 - - + -
216A LEU* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 5.2 5.9 + - - -
5A VAL* 4.5 15.8 + - + +
6A LEU* 1.3 74.3 - - - +
8A ILE* 1.3 61.6 + - - +
37A GLU* 3.4 26.0 - - + +
39A VAL* 4.0 12.1 - - + -
73A ASN* 2.8 42.2 + - - +
74A ARG* 3.2 23.2 + - - +
75A ALA* 3.8 10.1 + - - -
76A ASP* 2.8 65.2 + - - +
77A ILE* 3.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.3 3.4 - - + +
7A ARG* 1.3 74.5 - - - +
9A ALA* 1.3 64.3 + - - +
10A THR* 3.8 2.6 + - - +
20A ALA* 4.5 20.0 - - + +
23A VAL* 4.3 15.0 - - + -
24A LYS 4.6 2.9 - - - +
27A LEU* 4.6 4.7 - - + -
36A VAL* 3.7 30.1 - - + -
37A GLU 2.8 12.7 + - - +
38A LEU* 3.7 12.4 - - + -
39A VAL* 2.7 31.7 + - - +
77A ILE* 3.5 30.5 - - + -
79A VAL* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 1.3 75.8 - - - +
10A THR* 1.3 61.6 + - - +
39A VAL* 3.2 10.5 - - - +
41A MET* 4.2 9.2 - - + -
66A LEU* 3.9 26.2 - - + +
69A ALA* 4.5 5.8 - - + -
75A ALA* 3.6 22.4 - - + +
77A ILE 2.9 12.5 + - - +
78A ALA* 3.6 2.7 - - - -
79A VAL 3.4 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.2 10.3 - - - +
9A ALA* 1.3 77.5 - - - +
11A ARG* 1.3 76.0 + - - +
16A ALA* 3.4 21.1 + - - +
17A LEU* 4.3 7.6 - - + -
20A ALA* 4.0 23.7 + - + +
38A LEU* 5.2 3.6 - - + -
39A VAL 3.3 4.1 + - - +
40A PRO* 3.2 19.3 - - + +
41A MET* 2.7 33.5 + - - +
66A LEU* 3.8 13.7 - - - +
79A VAL* 4.7 10.3 + - - +
----------------------------------------------------------
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