Contacts of the strand formed by residues 44 - 49 (chain D) in PDB entry 1KGC
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 GLU 44 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 3.3 8.0 - - - -
36D ARG* 2.6 84.7 + - + +
37D GLN* 5.4 0.2 - - - -
38D LEU* 4.3 13.6 - - + +
41D GLN* 6.1 0.9 - - - +
42D GLY 4.7 4.6 - - - +
43D PRO* 1.3 77.1 - - - +
45D TYR* 1.3 68.7 + - - +
46D VAL* 3.9 0.5 - - - +
83D ARG* 5.7 2.0 + - - -
106E GLN 5.3 1.3 - - - -
108E PHE* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D HIS* 5.0 2.5 - + - -
34D TRP 4.3 0.4 - - - -
35D TYR* 3.4 35.4 - + + -
44D GLU* 1.3 81.0 - - - +
46D VAL* 1.3 74.9 + - - +
47D ILE* 3.4 26.8 - - - +
48D HIS* 2.7 44.7 + + + -
57D ASN* 5.6 1.3 - - - -
105E GLU* 3.6 44.2 - - + -
106E GLN 4.4 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TRP* 2.9 19.8 + - + +
35D TYR 4.0 1.6 - - - -
36D ARG* 3.7 45.1 - - + +
45D TYR* 1.3 86.8 - - - +
47D ILE* 1.3 66.5 + - + +
57D ASN* 3.3 16.8 + - - +
61D MET* 4.6 14.8 - - - -
62D ALA* 4.5 10.1 - - + -
75D LEU* 4.0 29.8 - - + -
77D LEU* 5.2 0.7 - - + -
88D TYR* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D HIS* 3.6 0.2 - - - -
34D TRP* 2.8 36.4 + - + +
45D TYR* 3.4 16.4 - - - +
46D VAL* 1.3 83.7 - - + +
48D HIS* 1.3 77.8 + - - +
55D VAL* 3.5 34.3 - - + +
56D ASN* 3.7 11.9 - - - -
57D ASN* 3.7 20.0 - - - +
62D ALA* 3.9 7.2 - - + +
63D SER* 4.3 0.7 - - - -
64D LEU* 4.1 18.2 - - + +
75D LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR* 3.8 25.8 - + - -
32D ILE 3.1 14.8 - - - +
33D HIS* 3.4 37.2 - + + -
45D TYR* 2.7 31.8 + + + -
47D ILE* 1.3 80.9 - - - +
49D GLY* 1.3 57.1 + - - +
55D VAL* 3.7 15.6 - - - +
64D LEU* 4.0 5.4 - - - -
99E ALA 4.7 14.6 + - - -
100E TYR* 6.4 0.7 - - - -
105E GLU* 5.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR* 3.6 14.5 - - - -
32D ILE* 2.9 30.2 + - - +
48D HIS* 1.3 77.8 - - - +
50D LEU* 1.3 62.1 + - - -
51D THR 3.6 2.0 - - - -
55D VAL* 4.5 10.3 - - - -
64D LEU* 3.5 17.2 - - - +
66D ILE* 4.0 2.8 - - - +
----------------------------------------------------------
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