Contacts of the strand formed by residues 87 - 93 (chain L) in PDB entry 3KDM
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 ASP 87 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 5.5 1.4 + - - -
39L GLN* 3.6 0.5 - - - -
40L GLN* 2.8 45.2 + - + +
42L PRO* 5.6 0.2 - - - +
86L ALA* 1.3 73.7 - - - +
88L TYR* 1.3 63.2 + - - +
89L TYR* 3.9 29.2 + - + -
105L GLY 6.1 0.4 - - - -
106L THR 3.3 5.0 - - - +
107L LYS* 3.3 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 2.9 9.9 + - - -
20L ILE* 3.7 18.8 - - + -
37L TRP* 4.7 4.7 - - + -
38L TYR 3.2 15.0 - - - +
39L GLN* 2.7 43.0 + - + -
49L MET* 5.0 1.6 - - + -
64L PHE* 3.8 23.2 - + - -
75L LEU* 3.6 20.4 - - + -
77L ILE* 3.8 8.3 - - + +
84L ASP 2.7 29.9 + - - -
86L ALA* 3.5 13.5 - - + -
87L ASP* 1.3 76.7 - - - +
89L TYR* 1.3 61.6 + - - +
105L GLY* 3.2 1.0 - - - -
106L THR 2.7 37.0 + - - +
108L VAL* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 3.3 10.9 + - - -
43H LYS 3.7 2.3 + - - -
44H GLY* 3.3 35.4 - - - -
45H LEU* 3.7 35.2 - - + -
6L GLN* 3.6 2.2 - - - -
37L TRP* 3.3 5.8 - - - -
38L TYR* 2.7 45.5 + - + -
40L GLN* 3.7 23.3 + - + -
87L ASP* 3.9 28.3 + - + +
88L TYR* 1.3 76.3 - - - +
90L CYS* 1.3 66.5 + - - +
102L PHE* 4.3 6.1 - + + -
103L GLY 3.4 19.1 - - - -
104L THR 4.0 2.9 - - - -
105L GLY* 3.5 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L LEU* 3.9 2.5 - - - -
6L GLN* 3.0 25.1 + - - -
22L CYS* 2.1 49.8 - - + -
35L VAL* 4.4 3.6 - - + -
36L SER 3.0 11.2 - - - +
37L TRP* 3.7 22.0 - - + -
38L TYR* 5.0 0.4 - - - -
89L TYR* 1.3 76.5 - - - +
91L SER* 1.3 63.9 + - - +
102L PHE* 3.5 6.1 - - - -
103L GLY* 2.8 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H TYR 4.0 0.3 + - - -
4L LEU* 3.7 6.7 - - - -
34L TYR 4.4 0.4 - - - -
35L VAL* 3.2 10.9 - - - +
36L SER* 2.8 44.7 + - - -
38L TYR* 3.7 2.6 - - - -
90L CYS* 1.3 76.9 - - - +
92L SER* 1.3 63.5 - - - +
100L TYR* 2.7 35.9 + - - -
101L VAL 3.1 15.7 - - - -
102L PHE* 3.9 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L LEU* 3.6 16.1 - - - +
28L ASP* 3.4 26.2 - - - +
29L VAL* 3.5 10.8 + - - -
32L TYR* 5.4 1.4 + - - +
34L TYR* 3.4 12.7 + - - +
35L VAL* 4.5 1.2 - - - +
91L SER* 1.3 76.4 - - - +
93L TYR* 1.3 80.9 + - - +
100L TYR* 3.2 9.7 - - - -
101L VAL* 2.8 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H TYR* 3.5 40.7 - + + -
28L ASP* 3.3 11.3 - - - +
32L TYR* 3.7 43.5 - + + -
34L TYR* 3.5 32.6 + + + +
92L SER* 1.3 96.1 + - - +
94L THR* 1.3 75.2 + - - +
95L SER* 3.3 29.4 - - - -
99L PRO* 3.4 14.4 - - + -
100L TYR* 4.5 0.2 - - - -
----------------------------------------------------------
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