Contacts of the strand formed by residues 22 - 28 (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 GLY 22 (chain s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17s LEU 3.9 1.0 - - - +
18s LYS* 3.7 2.3 - - - -
19s THR* 2.9 36.8 + - - +
20s THR 3.3 1.0 - - - -
21s ALA* 1.3 80.8 - - - +
23s ASP* 1.3 61.1 + - - -
24s ILE* 5.4 0.5 - - - +
140s ASN* 4.1 6.3 - - - -
99t VAL* 3.9 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17s LEU 3.7 5.2 - - - +
18s LYS* 4.7 5.4 - - + +
22s GLY* 1.3 72.5 - - - -
24s ILE* 1.3 60.3 + - - +
137s THR* 3.6 15.6 - - - -
140s ASN* 3.5 16.3 - - - +
99t VAL* 5.2 0.2 - - - +
100t TYR 3.9 17.6 + - - +
101t LYS* 4.5 3.8 - - - -
102t SER* 4.3 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16s LEU* 3.6 2.1 - - - -
17s LEU* 2.9 45.9 + - + +
22s GLY 5.4 0.7 - - - +
23s ASP* 1.3 74.9 - - - +
25s ASP* 1.3 61.0 + - - +
26s ILE* 3.7 4.6 + - + +
133s VAL* 5.8 6.1 - - + -
137s THR* 4.6 9.4 - - - +
140s ASN* 5.4 3.8 - - + -
141s MET* 5.6 9.4 - - + -
102t SER* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14s LYS* 6.0 3.4 - - + -
15s VAL 3.4 10.1 - - - +
16s LEU* 4.5 5.2 - - + +
23s ASP 4.3 0.2 - - - -
24s ILE* 1.3 71.0 - - - +
26s ILE* 1.3 61.8 + - - +
27s GLU* 3.6 1.7 + - - +
133s VAL* 3.7 5.6 - - - +
134s THR* 3.2 38.3 + - - -
137s THR* 4.5 10.9 - - - -
102t SER* 4.8 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14s LYS* 3.4 1.7 - - - -
15s VAL* 2.9 41.9 + - + +
17s LEU* 6.1 4.0 - - + -
24s ILE* 3.7 6.0 + - + +
25s ASP* 1.3 71.1 - - - +
27s GLU* 1.3 60.3 + - - +
28s LEU* 4.2 1.4 + - - +
131s GLY* 6.2 1.1 - - - -
132s LYS 3.4 12.1 - - - +
133s VAL* 4.6 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11s THR* 4.5 15.6 - - - -
13s GLY 3.3 11.4 - - - +
14s LYS* 4.1 10.3 - - + +
25s ASP 3.6 4.9 + - - +
26s ILE* 1.3 72.8 - - - +
28s LEU* 1.3 61.0 + - - +
131s GLY* 3.4 1.6 - - - -
132s LYS* 2.9 36.0 + - + +
134s THR* 5.6 7.2 - - - +
108t PRO* 5.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11s THR* 3.3 7.1 - - - -
12s ASN 2.8 35.3 + - - +
13s GLY* 2.9 11.6 + - - +
26s ILE 4.2 1.3 + - - +
27s GLU* 1.3 74.2 - - - +
29s TRP* 1.3 63.4 + - - +
30s SER* 3.6 2.5 - - - +
37s CYS* 4.5 13.7 - - + -
130s PHE 3.4 14.6 - - - +
131s GLY* 3.9 1.6 - - - -
----------------------------------------------------------
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