Contacts of the strand formed by residues 17 - 23 (chain b) 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 17 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13b GLY 5.6 1.1 - - - +
14b LEU* 3.5 22.4 + - + +
15b THR 3.4 1.8 - - - +
16b GLY* 1.3 78.3 - - - +
18b PRO* 1.4 62.2 - - - +
19b VAL* 3.8 1.3 + - + +
32b TYR* 4.3 1.8 - - - -
33b LEU* 2.5 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 18 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16b GLY 4.2 1.0 - - - -
17b LYS* 1.4 71.0 - - - +
19b VAL* 1.3 62.3 + - - +
31b GLY 3.5 10.5 - - - +
32b TYR* 4.3 5.4 - - + -
74b GLY* 4.0 15.4 - - - +
76b GLU* 4.8 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17b LYS 3.8 4.7 + - - +
18b PRO* 1.3 74.8 - - - +
20b MET* 1.3 63.6 + - - +
21b VAL* 4.0 1.8 + - + +
29b TYR 4.0 0.5 - - - +
30b LYS* 3.4 4.7 - - - +
31b GLY 3.1 30.3 + - - +
33b LEU* 5.5 6.3 - - + -
72b ILE* 5.1 8.3 - - + -
73b ARG 3.4 17.7 - - - +
74b GLY* 4.2 3.1 - - - -
76b GLU* 5.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19b VAL* 1.3 73.9 - - - +
21b VAL* 1.3 63.0 + - - +
22b LYS 4.3 0.2 + - - -
28b GLU* 6.0 3.1 - - + -
29b TYR 3.8 3.8 - - - -
30b LYS* 4.2 10.8 - - + +
72b ILE* 3.9 1.3 - - - -
73b ARG* 2.7 44.3 + - + +
75b VAL* 5.4 3.3 - - + +
76b GLU* 6.0 1.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19b VAL* 4.0 1.3 + - + -
20b MET* 1.3 73.9 - - - +
22b LYS* 1.3 60.7 + - - +
27b MET 4.8 0.2 - - - -
28b GLU* 3.2 11.8 - - - +
29b TYR* 2.8 46.9 + - + +
69b VAL* 6.4 1.6 - - + -
71b TYR 3.9 8.1 - - - +
72b ILE* 4.8 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20b MET 4.3 0.2 + - - -
21b VAL* 1.3 77.0 - - - +
23b LEU* 1.3 63.8 + - - +
26b GLY 6.3 0.4 - - - -
27b MET 3.8 4.7 - - - +
28b GLU* 4.7 3.6 - - + +
69b VAL* 3.9 3.5 - - - -
70b LEU* 2.9 29.3 + - + +
71b TYR* 3.3 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22b LYS* 1.3 78.0 - - - +
24b LYS* 1.3 55.9 + - - +
25b TRP* 3.1 9.9 - - + +
26b GLY* 2.9 22.0 + - - -
27b MET* 3.0 27.3 + - + +
68b ASN* 2.9 28.0 - - + +
69b VAL* 4.5 0.9 - - - +
70b LEU* 4.2 5.1 - - - +
----------------------------------------------------------
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