Contacts of the strand formed by residues 54 - 60 (chain A) in PDB entry 1KIT
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 SER 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 4.5 5.8 - - - +
52A ASN 3.0 10.2 + - - -
53A GLY* 1.3 73.2 + - - -
55A GLY* 1.3 61.7 + - - +
68A VAL* 4.0 0.2 - - - -
69A GLN* 2.5 61.8 + - - +
71A ILE* 5.1 0.9 - - - -
75A ALA* 3.5 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 5.1 1.6 - - - +
54A SER* 1.3 83.3 + - - +
56A VAL* 1.3 67.5 + - - +
66A TRP* 3.2 24.1 - - - -
67A LEU 3.2 12.3 - - - -
68A VAL* 4.6 0.2 - - - -
69A GLN* 3.6 4.9 - - - +
75A ALA* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 1.3 77.3 - - - +
57A LEU* 1.3 78.3 + - + +
58A THR* 3.2 10.8 + - - +
66A TRP* 3.2 15.8 - - + -
67A LEU* 2.8 36.9 + - + +
69A GLN* 4.3 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 6.0 0.2 - - - +
33A GLY 5.6 2.7 - - - +
34A ASP 4.7 5.2 - - - +
35A THR* 4.5 37.5 - - + +
38A ASP* 4.9 10.1 - - + +
39A SER* 4.9 10.5 - - - +
56A VAL* 1.3 86.4 - - + +
58A THR* 1.3 60.1 + - - +
65A ALA 3.4 10.5 - - - +
66A TRP* 3.2 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 3.2 4.7 + - - +
57A LEU* 1.3 77.1 - - - +
59A ASN* 1.3 66.3 + - - +
60A ALA* 3.9 17.5 - - + +
63A MET 3.1 3.2 - - - +
64A PRO* 3.5 0.3 - - - +
65A ALA* 2.9 33.9 + - - +
67A LEU* 3.2 40.6 - - + +
205A ALA* 5.7 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 5.8 1.2 - - - -
58A THR* 1.3 78.4 - - - +
60A ALA* 1.3 68.3 + - - +
61A ASP 3.1 1.0 + - - -
62A GLY* 2.8 28.8 + - - -
63A MET 3.0 7.4 - - - -
64A PRO* 2.8 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.8 13.4 - - + +
59A ASN* 1.3 73.1 - - - +
61A ASP* 1.3 59.4 + - + +
63A MET* 2.6 55.9 + - + +
101A LYS* 5.6 7.2 - - - +
----------------------------------------------------------
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