Contacts of the strand formed by residues 145 - 153 (chain D) in PDB entry 4P5K
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 PHE 145 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.7 40.6 - + + -
111D LYS 3.3 12.5 + - - -
112D PHE* 3.0 48.6 + - + +
113D PHE* 4.3 8.3 - + - -
115D PRO* 3.7 31.2 - - + -
137D PHE* 3.8 18.6 - - + -
138D LEU 3.4 16.8 - - - -
139D PRO* 4.3 11.4 - - + -
140D ARG* 4.4 5.2 - - - +
143D TYR 4.1 13.0 - - - -
144D SER* 1.3 82.3 + - - +
146D HIS* 1.3 60.5 + - - +
8E LEU* 4.5 1.1 - - + -
10E GLN* 3.9 19.7 - - - -
12E ARG* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 6.2 0.2 - - - -
28D GLU* 5.5 10.6 + - + +
108D HIS* 3.1 27.8 - + - +
109D ILE 3.1 13.0 - - - +
110D ASP* 3.0 25.8 - - - +
112D PHE* 3.6 3.1 - - - -
137D PHE* 3.6 2.8 - - - -
138D LEU* 2.8 71.0 + - + +
139D PRO 4.0 11.0 - - - -
140D ARG* 4.2 10.2 - - + +
145D PHE* 1.3 71.0 - - - +
147D LYS* 1.3 63.8 + - - +
148D PHE* 4.3 12.6 - + - -
147E ARG* 4.8 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D HIS* 3.5 4.9 - - - -
109D ILE* 3.0 32.2 + - + +
112D PHE* 4.1 13.2 - - + -
117D LEU* 4.3 11.1 - - + +
119D VAL* 5.7 0.6 - - - +
134D GLU* 2.7 29.0 + - - -
135D SER* 3.1 32.7 + - - +
136D LEU 4.0 7.9 - - - +
137D PHE* 3.7 39.8 - - + -
138D LEU* 4.9 0.7 - - - -
146D HIS* 1.3 82.7 - - - +
148D PHE* 1.3 74.2 - - - +
149D HIS* 3.7 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PHE* 5.0 0.2 - + - -
106D ILE* 3.8 20.0 - - + -
107D CYS 3.4 3.4 - - - +
108D HIS* 3.3 39.9 - + + -
134D GLU* 4.3 0.2 - - - -
135D SER* 2.8 35.7 + - - +
138D LEU* 3.7 26.7 - - + -
146D HIS* 4.3 7.9 - + - -
147D LYS* 1.3 75.6 - - - +
149D HIS* 1.3 72.7 + - - +
150D TYR* 3.5 29.2 - - + +
147E ARG* 3.4 38.4 - - + -
148E ASN 3.9 3.4 - - - -
149E GLY* 3.4 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 3.5 4.3 - - - +
107D CYS* 2.9 39.1 + - + +
109D ILE* 4.3 3.6 - - + -
119D VAL* 3.5 50.4 + - + +
121D TRP* 3.4 25.3 + - + +
132D VAL* 5.8 3.8 - - - +
133D ALA 3.6 6.0 + - - -
134D GLU* 3.6 32.9 - - + +
147D LYS* 3.7 24.6 + - + -
148D PHE* 1.3 91.1 - - - +
150D TYR* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS* 6.4 1.3 - - + -
104D THR* 4.2 15.7 - - + -
105D LEU 3.2 5.2 - - - +
106D ILE* 3.8 28.9 - - + -
121D TRP* 3.8 6.3 + - - -
131D GLY 4.4 0.9 - - - -
132D VAL* 3.4 4.9 - - - -
133D ALA* 2.8 51.2 + - + +
134D GLU* 4.1 7.4 - - - -
135D SER* 4.3 11.1 - - - -
148D PHE* 3.5 27.1 - - + +
149D HIS* 1.3 76.6 - - - +
151D LEU* 1.3 61.4 + - - +
152D THR* 6.2 1.3 - - + -
148E ASN 2.6 29.2 + - - -
149E GLY* 3.3 20.8 + - - -
150E ASP* 4.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D THR* 3.5 2.6 - - - +
105D LEU* 2.9 40.4 + - + +
121D TRP* 3.7 43.9 - - + +
128D VAL* 3.7 21.1 - - + -
130D GLU 3.4 25.1 - - - +
131D GLY 3.3 2.9 - - - +
132D VAL* 3.9 7.9 - - + -
150D TYR* 1.3 74.8 - - - +
152D THR* 1.3 74.9 + - - +
153D PHE* 3.7 4.3 - - + -
161D TYR* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN 3.4 8.1 - - - +
104D THR* 3.9 17.9 - - + +
130D GLU 5.0 1.0 - - - +
131D GLY* 2.8 34.6 + - - +
150D TYR* 5.9 1.1 - - + -
151D LEU* 1.3 81.0 - - - +
153D PHE* 1.3 66.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PRO* 4.6 3.6 - - + -
97D VAL* 4.7 1.3 - - + -
102D PRO* 3.5 2.2 - - - +
103D ASN* 2.7 62.6 + - + -
104D THR 3.8 1.3 - - - -
105D LEU* 3.5 31.4 - - + -
151D LEU* 3.7 17.5 - - + +
152D THR* 1.3 76.9 - - - +
154D VAL* 1.3 67.5 + - - +
155D PRO* 3.5 28.7 - - + +
156D SER 5.3 0.4 - - - -
161D TYR* 3.7 37.5 - + + +
178D TRP* 4.0 32.8 - + - -
----------------------------------------------------------
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