Contacts of the strand formed by residues 89 - 96 (chain A) in PDB entry 1KRB
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 GLY 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 4.3 7.6 - - - -
86A PHE* 2.9 37.3 + - - +
87A PRO 3.5 2.2 + - - -
88A ASP* 1.3 76.1 - - - +
90A SER* 1.3 66.9 + - - -
91A LYS* 3.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 4.4 16.2 - - - -
84A ALA 3.3 13.0 + - - -
85A THR* 4.2 12.0 + - - +
89A GLY* 1.3 71.6 - - - -
91A LYS* 1.3 72.6 + - - +
462C ASN* 4.6 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.6 18.2 - - + -
82A VAL 4.0 0.2 - - - +
83A GLU* 3.2 27.5 - - - -
84A ALA 3.3 9.4 + - - -
86A PHE* 3.5 29.2 - - + -
88A ASP* 3.1 42.4 + - - +
89A GLY* 3.6 8.3 - - - +
90A SER* 1.3 84.9 + - - +
92A LEU* 1.3 61.3 - - - +
93A VAL 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.8 16.3 - - - +
57A MET* 4.4 4.2 - - - +
81A GLN* 3.9 19.1 - - + +
82A VAL 4.0 3.4 - - - +
83A GLU* 3.7 19.0 + - + +
91A LYS* 1.3 73.4 - - - +
93A VAL* 1.3 64.9 + - - +
94A THR* 3.9 15.8 + - - +
464C SER* 3.8 15.9 - - - +
465C ILE* 3.8 20.2 - - + -
468C PRO* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.6 32.5 - - + +
53A VAL* 4.4 9.6 - - + +
56A LEU* 3.9 21.1 - - + -
57A MET* 4.0 18.8 - - + +
80A ILE 3.6 1.2 - - - +
81A GLN* 3.2 6.6 - - - +
82A VAL* 3.0 33.2 + - + +
83A GLU* 5.7 0.2 - - - -
84A ALA* 6.0 0.4 - - + +
86A PHE* 3.6 33.2 - - + -
92A LEU* 1.3 76.5 - - - +
94A THR* 1.3 62.3 + - - +
95A VAL* 4.3 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.5 34.8 - - - +
79A ASP* 4.6 6.1 - - - +
80A ILE 3.5 2.7 - - - +
81A GLN* 3.1 34.6 + - + +
92A LEU* 3.9 14.8 + - - +
93A VAL* 1.3 75.9 - - - +
95A VAL* 1.3 64.2 + - - +
96A HIS* 3.7 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 5.3 0.9 - - + -
43A ILE* 3.6 31.0 - - + -
56A LEU 4.4 4.3 - - - +
57A MET 3.8 7.2 - - - +
60A GLY* 3.7 21.3 - - - -
61A ARG* 3.5 31.6 - - + -
79A ASP* 3.0 6.0 - - - -
80A ILE* 2.9 44.3 + - + +
93A VAL* 4.3 8.7 - - + -
94A THR* 1.3 76.6 - - - +
96A HIS* 1.3 60.1 + - - +
98A PRO* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 5.2 0.4 + - - -
61A ARG* 3.2 20.9 + - - +
78A PRO 3.7 5.5 + - - +
79A ASP* 4.0 13.4 + - + +
94A THR* 3.7 32.3 - - + +
95A VAL* 1.3 72.3 - - - +
97A ASN* 1.3 81.5 + - - +
98A PRO 3.3 0.3 - - - -
----------------------------------------------------------
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