Contacts of the strand formed by residues 123 - 128 (chain E) in PDB entry 3KHU
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 123 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 3.7 48.8 - + + -
82E ALA 4.7 1.2 - - - +
83E ASP* 4.6 7.3 - - - +
121E ASN 3.6 1.1 + - - +
122E GLY* 1.3 70.2 - - - -
124E LYS* 1.3 73.8 + - - +
125E ILE* 3.6 28.6 - - + +
153E ASN* 3.4 28.9 - - + -
155E GLN* 3.7 20.9 - - + +
187E GLU* 4.0 14.0 + - - -
190E ARG* 4.6 17.5 - - - +
191E ALA* 3.8 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ILE 3.2 18.1 + - - +
80E LYS 2.8 24.1 + - - -
81E GLU 4.3 0.4 - - - -
82E ALA 2.6 27.3 + - - +
83E ASP 3.4 9.9 - - - +
85E VAL* 4.3 12.8 - - + -
116E ILE* 5.5 0.7 - - + -
120E SER* 3.5 35.7 - - - +
121E ASN 4.2 12.6 + - - +
122E GLY 3.8 0.8 + - - -
123E TYR* 1.3 83.9 + - - +
125E ILE* 1.3 67.0 + - - +
126E VAL* 4.0 2.4 + - + -
153E ASN 3.2 7.1 + - - +
154E LEU* 3.4 20.4 - - + +
155E GLN* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 4.1 14.6 - - + -
4E ILE* 4.1 11.4 - - + -
83E ASP 2.9 9.3 + - - +
84E LEU* 3.2 24.0 - - + +
85E VAL* 2.8 32.4 + - - +
123E TYR* 3.6 26.7 - - + +
124E LYS* 1.3 73.6 - - - +
126E VAL* 1.3 60.4 + - - +
127E THR* 3.7 1.8 - - - +
155E GLN* 3.5 5.4 - - + +
157E LEU* 3.6 30.3 - - + -
191E ALA* 4.0 14.4 - - + +
194E ALA* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL* 3.3 15.0 - - + +
87E ILE* 3.9 27.6 - - + -
116E ILE* 4.0 23.6 - - + -
124E LYS* 4.9 0.9 - - + -
125E ILE* 1.3 76.3 - - - +
127E THR* 1.3 63.4 + - - +
140E ILE* 4.7 6.7 - - + -
144E PHE* 4.0 32.3 - - + -
154E LEU* 4.3 14.6 - - + -
155E GLN 2.6 15.3 + - - +
156E VAL* 3.2 6.9 - - + +
157E LEU 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LEU* 3.2 22.8 - - - +
85E VAL 2.9 9.3 + - - -
86E PHE* 3.4 26.2 - - + -
87E ILE* 2.8 28.0 + - - -
125E ILE* 3.7 6.9 - - - +
126E VAL* 1.3 74.3 + - - +
128E GLU* 1.3 65.7 + - - +
129E LYS 3.4 0.9 + - - -
157E LEU* 3.4 15.5 - - + +
159E ASN* 3.3 36.3 - - + +
195E LEU* 4.1 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 3.9 9.6 - - + -
109E ILE* 5.9 1.3 - - + -
126E VAL* 4.3 0.8 + - - +
127E THR* 1.3 71.1 - - - +
129E LYS* 1.3 58.7 - - - +
130E SER 4.4 1.3 - - - +
132E VAL* 3.7 23.7 - - + +
136E ALA* 3.0 16.1 - - - +
137E ALA* 3.0 32.2 + - + +
140E ILE* 3.6 21.4 - - + +
156E VAL* 5.2 1.1 - - + -
157E LEU 2.9 16.3 + - - +
158E SER* 3.6 13.2 + - - +
159E ASN* 2.8 31.4 + - - -
160E PRO* 4.1 0.5 - - - +
217E GLU* 2.7 29.8 - - - +
----------------------------------------------------------
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