Contacts of the strand formed by residues 19 - 29 (chain L) in PDB entry 6K7O
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 19 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.6 8.7 - - - +
8C PRO* 5.8 2.2 - - + -
22C THR* 5.2 0.2 - - - -
11L LEU* 4.4 16.4 - - + -
13L ALA* 3.5 33.2 - - + -
17L ASP* 4.3 6.7 - - + +
18L ARG* 1.3 76.0 - - - +
20L THR* 1.3 63.2 + - - +
21L ILE* 4.9 11.4 - - + -
74L LEU 5.5 0.2 - - - +
75L THR* 3.3 4.5 - - - +
76L ILE* 2.9 65.1 + - + -
79L LEU* 4.1 14.8 - - + -
108L VAL* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 5.9 0.2 + - - -
8C PRO* 6.1 2.0 - - - +
20C THR* 4.3 36.4 + - + +
22C THR* 3.9 17.7 + - - -
8L PRO* 4.8 8.8 - - - +
11L LEU* 5.3 2.7 - - - +
18L ARG* 4.1 6.8 + - - -
19L VAL* 1.3 76.2 + - - +
21L ILE* 1.3 72.6 + - - +
22L THR* 4.2 2.4 + - - -
73L THR* 4.1 17.3 - - + -
74L LEU 3.2 4.5 - - - +
75L THR* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 4.4 0.2 - - - +
7L SER 3.9 6.3 - - - +
8L PRO* 5.0 1.1 - - - -
11L LEU* 4.6 8.3 - - + -
19L VAL* 4.9 8.7 - - + -
20L THR* 1.3 76.8 - - - +
22L THR* 1.3 71.4 + - - +
36L TRP* 4.2 13.2 - - + -
73L THR* 3.1 6.9 - - - -
74L LEU* 2.7 56.3 + - + +
76L ILE* 5.3 2.7 - - + -
87L TYR* 3.9 38.6 - - + -
106L THR* 3.2 42.2 - - + +
108L VAL* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 3.4 48.2 + - + +
19C VAL* 4.9 0.2 - - - -
20C THR* 3.5 20.0 + - - +
5L THR 4.6 0.2 - - - -
6L GLN* 3.3 6.2 - - - +
7L SER* 3.0 35.9 + - - -
20L THR* 4.6 1.6 + - - +
21L ILE* 1.3 77.4 - - - +
23L CYS* 1.3 68.5 + - - +
24L GLN* 5.1 2.9 - - + +
36L TRP* 4.2 1.6 - - - -
71L ASP* 5.1 3.1 - - + -
72L PHE 3.3 14.8 - - - +
73L THR* 4.3 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L MET* 3.6 23.1 - - - -
5L THR 3.3 5.6 - - - -
6L GLN* 4.4 0.4 - - + -
22L THR* 1.3 74.7 - - - +
24L GLN* 1.3 61.7 + - - +
34L LEU* 4.6 5.4 - - - -
36L TRP* 3.4 21.3 - - + -
71L ASP* 3.7 0.3 - - - -
72L PHE* 2.8 44.1 + - + +
89L CYS* 2.0 48.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY 3.8 12.1 + - - +
17C ASP* 4.3 1.9 - - - -
18C ARG* 3.8 38.1 + - + +
77C SER 4.6 6.7 + - - -
3L GLN 3.8 0.2 - - - +
4L MET* 3.3 10.6 - - - +
5L THR* 2.5 54.3 + - + +
22L THR* 4.3 3.3 - - + -
23L CYS* 1.3 73.5 - - - +
25L ALA* 1.3 62.8 + - - +
70L THR* 3.3 4.3 - - - +
71L ASP* 3.1 28.8 + - + +
72L PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L ILE* 5.0 0.9 - - + -
3L GLN 3.7 3.8 - - - -
4L MET* 3.8 22.2 - - + -
24L GLN* 1.3 79.4 + - - +
26L SER* 1.3 64.6 + - - +
27L GLU 3.3 21.3 + - - +
29L ILE* 4.1 10.3 - - + -
69L GLY 4.7 1.1 - - - +
70L THR* 2.9 31.8 + - - +
72L PHE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L ASP 4.0 4.3 + - - -
2L ILE* 3.3 13.8 - - - +
3L GLN* 3.1 51.8 + - - -
25L ALA* 1.3 73.3 - - - +
27L GLU* 1.3 62.8 + - - +
70L THR* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.3 15.2 + - - -
1L ASP 3.8 7.8 - - - +
2L ILE* 3.5 39.8 - - + +
25L ALA* 3.1 9.5 - - - +
26L SER* 1.3 81.2 - - - +
28L SER* 1.3 75.5 + - - +
29L ILE* 3.3 15.8 - - - +
70L THR* 3.8 8.1 - - - -
93L TYR* 5.0 2.3 - - - -
94L ASP* 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L GLU* 1.3 82.8 - - - +
29L ILE* 1.3 61.5 + - - +
69L GLY* 3.7 20.1 - - - -
70L THR* 3.7 15.0 - - - +
93L TYR* 3.8 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L ILE* 4.9 10.3 - - + -
4L MET* 4.7 7.4 - - + -
25L ALA* 4.1 10.8 - - + -
27L GLU 3.3 17.3 - - - +
28L SER* 1.3 75.3 - - - +
30L ASN* 1.3 75.7 + - - +
31L SER 3.4 2.1 + - - -
33L TYR 4.5 2.2 - - - +
34L LEU* 3.7 33.2 - - + -
69L GLY* 3.2 22.2 + - - +
72L PHE* 3.8 20.0 - - + -
91L GLN* 4.0 17.7 - - + -
93L TYR* 3.8 26.0 - - + -
----------------------------------------------------------
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