Contacts of the strand formed by residues 68 - 75 (chain D) in PDB entry 1KD1
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 THR 68 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2719A A 5.7 5.2 - - + -
50D HIS* 3.5 38.1 - - + -
51D VAL 3.6 5.8 - - - +
52D VAL* 4.3 11.0 - - + +
67D GLU* 1.3 75.8 - - - +
69D VAL* 1.3 68.4 + - - +
70D PRO* 4.4 3.2 - - - +
81L ARG* 5.4 5.2 + - - -
83L PRO 3.2 12.0 + - - +
84L ASP* 3.0 33.0 + - - +
85L GLY* 4.0 6.7 - - - -
16V GLY* 3.7 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D HIS* 3.3 3.8 - - - -
51D VAL* 2.9 42.8 + - + +
53D LEU* 4.4 18.8 - - + -
67D GLU* 4.1 23.8 - - + +
68D THR* 1.3 83.7 - - - +
70D PRO* 1.3 84.5 - - + +
71D VAL* 4.3 6.7 - - + -
270D ILE* 4.8 1.6 - - + -
298D LYS* 3.8 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2719A A 3.1 51.1 - - + +
2764A C 3.8 21.5 - - - +
2765A C 4.8 12.1 - - - +
48D MET* 3.9 9.6 - - + -
49D THR 3.9 4.9 - - - +
50D HIS* 4.4 0.4 - - - -
68D THR* 4.4 3.4 - - + +
69D VAL* 1.3 94.5 - - + +
71D VAL* 1.3 67.1 + - - +
298D LYS* 5.9 0.4 - - - -
299D GLY* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D MET* 3.3 8.1 - - - +
49D THR* 2.8 43.3 + - - +
50D HIS* 5.0 0.4 - - - -
51D VAL* 3.5 32.1 - - + +
69D VAL* 3.7 5.2 - - + +
70D PRO* 1.3 86.3 - - - +
72D THR* 1.3 66.3 + - - +
73D VAL* 3.8 1.4 + - + +
270D ILE* 4.4 11.9 - - + -
296D LEU* 3.5 44.2 - - + -
297D VAL 3.2 14.4 - - - +
299D GLY 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2717A C 5.3 0.2 + - - -
45D LYS* 4.2 23.5 + - + -
47D GLY 3.2 17.5 - - - +
48D MET* 3.4 12.7 - - + +
71D VAL* 1.3 75.5 - - - +
73D VAL* 1.3 70.7 + - - +
74D ILE* 3.6 13.5 + - + +
295D THR 3.6 0.5 - - - +
297D VAL* 2.7 36.6 + - - +
299D GLY 2.8 21.8 + - - -
300D SER* 3.7 8.1 - - - -
301D VAL* 4.1 17.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 2.9 28.8 + - + -
47D GLY 2.7 15.7 + - - +
49D THR* 4.0 16.6 - - - +
71D VAL 4.6 1.6 - - - +
72D THR* 1.3 73.7 - - - +
74D ILE* 1.3 65.9 + - - +
278D PRO* 4.3 22.7 - - + -
284D PHE* 3.9 24.5 - - + -
290D VAL* 4.3 23.6 - - + -
294D TYR* 4.7 9.4 - - + -
295D THR 3.9 2.7 - - - -
296D LEU* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLY* 4.0 0.7 - - - -
44D TYR 3.6 22.0 - - - +
45D LYS* 4.3 7.2 - - - -
72D THR* 4.1 13.0 - - + +
73D VAL* 1.3 80.7 - - - +
75D GLU* 1.3 65.1 + - - +
76D THR* 3.2 20.8 + - + +
202D VAL* 5.2 0.4 - - + -
294D TYR* 3.5 2.6 - - - -
295D THR 2.8 38.7 + - - +
297D VAL* 3.9 14.1 - - + -
301D VAL* 4.1 20.9 - - + -
309D VAL* 3.7 20.2 - - + -
311D PHE* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLY* 3.1 2.8 - - - -
44D TYR* 2.9 40.1 + - + +
46D ALA* 4.5 2.9 - - + +
73D VAL* 5.4 0.2 - - + -
74D ILE* 1.3 68.8 - - - +
76D THR* 1.3 58.8 + - - +
77D PRO* 3.1 16.4 - - + +
150D ALA 5.6 0.7 - - - +
151D VAL* 3.1 24.0 - - + +
152D PRO* 5.4 3.6 - - - +
153D SER* 4.1 4.2 + - - -
287D TYR* 2.6 36.8 + - + +
289D GLU 4.4 2.5 - - - +
290D VAL* 3.8 39.2 - - + +
291D ASP 4.2 7.4 + - - -
292D GLY* 4.6 6.9 + - - -
293D PRO 3.6 11.4 - - - +
294D TYR* 4.3 1.3 - - + +
----------------------------------------------------------
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