Contacts of the strand formed by residues 14 - 19 (chain s) in PDB entry 6FF7
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 14 (chain s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13s GLY* 1.3 74.6 - - - +
15s VAL* 1.3 61.3 + - - +
25s ASP* 6.0 3.6 - - + -
26s ILE 3.4 9.4 - - - +
27s GLU* 4.2 11.0 - - + -
28s LEU* 6.0 0.2 - - - -
166s VAL* 4.4 0.2 - - - -
167s LEU* 3.0 15.5 + - + +
168s PHE* 2.9 36.7 + - + +
105t SER 4.8 9.2 - - - +
106t ALA* 4.8 13.0 - - - +
107t LYS 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14s LYS* 1.3 74.4 - - - +
16s LEU* 1.3 61.9 + - - +
17s LEU* 5.7 0.7 - - + -
25s ASP* 3.4 6.1 - - - +
26s ILE* 2.9 39.2 + - + +
41s ILE* 6.5 0.4 - - - -
44s CYS* 5.4 10.3 - - + -
164s CYS* 6.5 0.2 - - + -
165s GLU 3.3 14.1 - - - +
166s VAL* 4.4 6.1 - - + -
167s LEU* 4.0 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15s VAL* 1.3 75.8 - - - +
17s LEU* 1.3 62.2 + - - +
18s LYS 4.4 0.2 - - - -
24s ILE 3.6 5.2 - - - +
25s ASP* 4.5 5.6 - - + +
163s SER 5.6 0.2 - - - -
164s CYS* 3.4 3.8 - - - +
165s GLU* 2.8 52.5 + - + +
167s LEU* 4.7 5.1 - - + +
102t SER* 6.5 1.1 - - - -
104t ARG* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15s VAL 5.7 0.2 - - - -
16s LEU* 1.3 77.1 - - - +
18s LYS* 1.3 61.1 + - - +
19s THR 4.0 0.3 + - - -
22s GLY 3.9 1.0 - - - +
23s ASP* 3.7 2.1 - - - -
24s ILE* 2.9 45.8 + - + +
26s ILE* 6.1 4.0 - - + -
163s SER 3.7 7.0 - - - +
164s CYS* 5.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17s LEU* 1.3 72.7 - - - +
19s THR* 1.3 56.5 + - - +
22s GLY 3.7 5.2 - - - +
23s ASP* 4.7 5.2 - - + +
161s ILE* 3.5 4.9 - - - +
162s LYS* 2.7 37.0 + - + -
163s SER* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 19 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17s LEU 4.0 1.0 + - - -
18s LYS* 1.3 76.6 - - - +
20s THR* 1.3 61.5 + - - +
21s ALA* 3.1 12.8 - - - -
22s GLY* 2.9 28.4 + - - +
159s HIS* 4.8 7.4 - - - -
160s LYS 3.4 19.3 - - - -
161s ILE* 4.6 2.7 - - - -
162s LYS* 4.5 3.4 - - - +
----------------------------------------------------------
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