Contacts of the strand formed by residues 89 - 96 (chain H) in PDB entry 3KC3
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 LYS 89 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H GLN* 2.7 40.5 + - - +
81H ILE 3.8 2.0 - - - -
82H PHE* 3.6 22.0 - - + -
88H GLU* 1.3 81.0 - - - +
90H PHE* 1.3 68.4 + - - +
140H CYS* 3.4 23.4 + - + +
142H ASP* 3.4 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H TYR* 4.3 4.9 - + + -
79H LEU 3.7 0.3 - - - +
80H GLN* 3.8 3.3 - - - +
81H ILE* 2.9 53.9 + - + +
83H ASN* 4.1 24.0 - - + -
88H GLU* 3.6 49.1 - - + -
89H LYS* 1.3 80.8 - - - +
91H ALA* 1.3 59.9 + - - +
119H ARG* 5.2 3.4 - - - -
121H VAL* 3.6 31.0 - - + -
137H VAL* 4.0 12.6 - - + -
138H MET 3.6 14.6 - - - +
139H GLU* 4.2 8.5 - - + -
140H CYS* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LEU* 4.4 8.5 - - + -
78H VAL* 3.8 13.5 - - + -
79H LEU 3.3 5.4 - - - +
81H ILE* 4.3 0.9 - - - -
90H PHE* 1.3 74.6 - - - +
92H LEU* 1.3 60.6 + - - +
137H VAL* 3.2 8.5 - - - +
138H MET* 2.8 43.9 + - + +
139H GLU 3.9 1.3 - - - +
140H CYS* 4.2 2.6 - - - +
500H MK2 3.8 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ILE* 3.9 22.4 - - + -
65H VAL* 4.4 18.2 - - + -
77H LYS 3.5 1.7 - - - +
78H VAL* 2.9 9.7 - - - +
79H LEU* 2.8 39.5 + - + +
81H ILE* 3.7 29.8 - - + -
91H ALA* 1.3 77.2 - - - +
93H LYS* 1.3 61.9 + - - +
94H MET* 3.4 26.3 + - + +
135H LEU* 3.7 19.5 - - + -
136H ILE 3.2 29.2 - - - +
137H VAL* 4.0 2.7 - - + -
138H MET* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H GLY 4.4 2.0 - - - -
74H ILE* 4.3 3.4 - - - +
75H ASN 3.6 32.6 - - - +
77H LYS 3.8 3.4 - - - +
78H VAL* 4.3 9.2 - - + +
92H LEU* 1.3 73.6 - - - +
94H MET* 1.3 67.6 + - - +
95H LEU* 3.4 11.6 + - + +
104H GLU* 2.7 38.6 + - - +
134H LEU 3.5 0.3 - - - +
135H LEU* 3.5 4.2 - - - -
136H ILE* 2.8 48.7 + - + +
138H MET* 4.0 14.8 - - + +
207H ASP* 4.0 8.5 + - - -
500H MK2 3.4 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H VAL* 6.2 1.1 - - - -
75H ASN* 3.8 14.2 - - - +
76H GLY* 4.6 1.0 + - - -
77H LYS* 3.5 37.6 + - + +
79H LEU* 4.6 20.0 - - + -
92H LEU* 3.4 39.9 - - + +
93H LYS* 1.3 72.0 - - - +
95H LEU* 1.3 69.5 + - - +
96H GLN 4.2 0.5 + - - -
128H TYR* 6.4 3.4 - - - -
134H LEU 4.2 0.2 - - - -
135H LEU* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ASN* 3.4 41.5 - - + +
93H LYS* 3.4 13.6 + - + -
94H MET* 1.3 77.7 - - - +
96H GLN* 1.3 62.5 + - - +
101H ALA* 4.0 33.0 - - + +
104H GLU* 3.5 28.7 - - - +
105H VAL* 4.1 3.1 - - + -
133H CYS* 3.4 9.3 - - - +
134H LEU* 2.8 51.8 + - + +
135H LEU* 4.4 0.8 - - - +
136H ILE* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LYS* 4.2 8.3 + - - -
75H ASN* 6.0 0.4 - - - +
94H MET 4.2 0.8 + - - -
95H LEU* 1.3 72.9 - - - +
97H ASP* 1.3 71.0 + - - +
98H CYS* 3.5 8.0 - - + -
101H ALA* 3.2 15.4 - - - +
131H ARG* 3.2 57.4 + - - +
132H LYS 3.9 4.3 + - - +
133H CYS* 4.3 10.7 - - - -
----------------------------------------------------------
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