Contacts of the strand formed by residues 120 - 129 (chain C) in PDB entry 1KN0
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 TYR 120 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.9 14.4 - + - -
85B ALA* 2.8 51.6 - - + +
86B HIS* 3.1 28.5 + - - -
87B SER* 3.9 12.8 + - - -
112B ARG* 5.0 7.6 + - - +
114B GLN* 3.7 27.9 + - - +
112C ARG* 3.6 45.1 - - + +
113C VAL 3.2 13.7 - - - +
114C GLN* 4.2 2.0 - - - +
118C GLY 3.2 19.1 - - - +
119C SER* 1.3 77.9 + - - +
121C HIS* 1.3 66.3 + - - +
158C PHE* 4.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 4.8 0.2 - - - -
81B TYR 4.1 4.9 - - - -
84B TRP* 3.2 47.0 + + - -
86B HIS* 2.9 39.9 - + - +
112C ARG* 3.6 2.1 - - - -
113C VAL* 2.9 32.8 + - - +
119C SER* 4.9 0.2 - - - -
120C TYR* 1.3 78.4 - - - +
122C GLU* 1.3 61.9 + - - +
154C ALA* 3.8 12.9 - - - +
157C SER* 3.4 34.1 - - - -
158C PHE* 3.5 40.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 3.0 31.9 + - - +
87B SER* 3.2 21.7 - - - -
88B ILE* 2.6 53.6 + - + +
147B VAL* 4.8 0.3 - - - +
89C THR* 2.7 38.1 + - - +
110C PHE* 4.2 6.1 - - + +
111C VAL 3.3 13.7 - - - +
112C ARG* 3.8 15.4 - - + +
121C HIS* 1.3 76.7 - - - +
123C ASP* 1.3 65.6 + - - +
154C ALA* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 4.6 6.8 - - - -
88B ILE* 3.7 12.2 - - - +
147B VAL* 3.8 11.9 - - - +
148B THR* 5.3 1.2 + - - -
151B LEU* 5.9 0.7 - - - +
110C PHE* 3.4 4.0 - - - +
111C VAL* 3.0 34.0 + - - +
122C GLU* 1.3 76.6 - - - +
124C VAL* 1.3 78.3 + - - +
150C GLY* 4.3 2.4 - - - +
153C ARG* 3.2 50.2 + - + +
154C ALA* 3.8 24.3 - - + +
157C SER* 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 4.0 4.3 - - + -
91B GLN* 3.7 9.0 - - - +
143B ARG* 4.0 17.0 - - + +
144B LYS* 4.3 7.7 - - + -
147B VAL* 2.9 37.9 - - + -
108C CYS* 4.4 6.1 - - + -
109C ALA 3.2 7.9 - - - +
110C PHE* 3.4 31.4 - - + -
123C ASP* 1.3 87.1 + - - +
125C GLY* 1.3 68.8 + - - +
150C GLY* 4.0 2.7 - - - -
153C ARG* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 4.7 1.3 - - - -
108C CYS* 3.3 7.8 - - - +
109C ALA 2.7 28.6 + - - +
124C VAL* 1.3 79.0 - - - +
126C TYR* 1.3 61.3 + - - +
146C ALA 3.3 22.2 - - - -
149C ASP* 3.4 6.3 - - - -
150C GLY* 3.3 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 3.7 15.9 - - - -
139B LEU* 3.2 24.6 - - + +
140B GLU* 3.5 45.4 - - + +
143B ARG* 3.6 19.3 - - + -
144B LYS* 4.2 4.9 - - + -
94C ASP* 2.5 35.8 + - - +
95C PHE* 4.1 0.7 - - - -
106C GLY* 3.7 10.8 - - - -
107C VAL 3.2 25.6 - - - -
108C CYS* 3.5 13.9 - - + -
124C VAL* 5.8 0.4 - - + -
125C GLY* 1.3 73.4 - - - -
127C GLY* 1.3 70.2 + - - +
128C VAL* 3.8 13.4 + - + +
145C GLU* 4.1 2.6 - - - +
146C ALA* 3.5 5.0 + - - +
149C ASP* 2.9 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY* 3.8 1.6 - - - -
107C VAL 2.7 33.2 + - - +
126C TYR* 1.3 73.6 - - - +
128C VAL* 1.3 67.3 + - - +
142C ALA* 3.2 27.3 - - - +
145C GLU* 3.8 7.2 - - - -
146C ALA* 3.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 3.4 31.2 - - + -
137B LEU* 4.6 11.0 - - + -
140B GLU* 4.9 8.7 - - - +
105C VAL 3.5 5.4 - - - +
126C TYR* 3.8 20.9 - - + +
127C GLY* 1.3 81.7 - - - +
129C SER* 1.3 60.2 - - - +
130C GLU* 3.5 22.9 - - + +
141C LYS* 2.8 37.6 + - - +
142C ALA* 4.0 3.9 - - - +
145C GLU* 3.6 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE 3.4 1.1 - - - +
104C TYR* 3.4 1.4 - - - -
105C VAL* 2.8 37.5 + - - +
128C VAL* 1.3 77.9 - - - +
130C GLU* 1.3 62.6 + - - +
131C GLY 4.6 0.5 + - - -
132C LEU* 3.9 13.7 - - - +
138C SER* 3.1 50.4 + - - -
141C LYS* 3.9 14.1 - - - +
142C ALA* 4.7 0.2 - - - -
----------------------------------------------------------
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