Contacts of the strand formed by residues 142 - 146 (chain D) in PDB entry 5HP1
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 ILE 142 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C THR* 4.4 14.4 - - + -
49D LYS* 4.1 19.7 - - + -
131D THR* 3.6 0.7 - - - +
132D ILE* 3.0 38.1 + - + +
139D THR* 4.2 14.4 - - + -
140D PRO 3.5 16.4 - - - +
141D GLY* 1.3 74.8 - - - +
143D ARG* 1.3 62.0 + - - +
144D TYR* 3.6 38.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TRP* 3.0 26.6 - - - +
90C VAL* 3.8 26.2 - - + -
49D LYS* 3.5 8.0 - - - +
50D ILE* 2.9 42.8 + - + +
51D GLY 3.0 24.9 + - - -
52D PRO* 4.5 1.8 - - - -
54D ASN* 3.0 25.7 + - - -
56D TYR 2.6 23.2 + - - -
57D ASN* 2.8 28.7 + - - -
129D ALA* 3.3 16.7 - - - +
130D PHE 3.3 5.1 + - - +
131D THR* 3.4 16.2 - - + +
141D GLY 3.8 1.0 + - - -
142D ILE* 1.3 73.6 - - - +
144D TYR* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D CYS* 4.4 12.3 + - + +
39D THR* 5.4 1.9 + - - -
42D GLU* 4.0 17.8 + - + -
47D ILE* 3.4 27.1 - - + -
48D SER* 3.4 16.4 - - - +
49D LYS* 3.5 38.3 + - + -
50D ILE* 3.4 8.8 - - - +
129D ALA* 3.3 5.5 - - - -
130D PHE* 3.0 59.5 + + + -
132D ILE* 3.8 20.9 - - + +
142D ILE* 3.6 33.7 - - + +
143D ARG* 1.3 74.3 - - - +
145D GLN* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.1 10.4 - - - +
48D SER* 3.0 41.1 + - - +
50D ILE* 3.6 26.9 - - + +
54D ASN* 3.5 8.7 + - - -
122D GLU* 4.8 6.7 + - - -
125D ARG* 3.8 33.0 - - - +
126D LYS* 3.3 22.9 - - - +
128D THR* 4.0 7.2 - - - +
129D ALA* 4.5 4.3 - - - -
130D PHE* 5.0 0.2 - - - -
144D TYR* 1.3 74.8 - - - +
146D TYR* 1.3 66.2 + - - +
147D ASN* 4.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D MET* 3.8 20.5 - - + +
46D LYS 3.8 6.7 - - - -
47D ILE* 3.8 11.0 - - + -
73D LYS* 3.0 30.2 + - - -
75D VAL* 3.9 7.1 - - + +
77D PHE* 4.4 8.7 - + - -
116D PHE* 4.0 9.0 - + - -
120D LEU* 4.1 2.3 - - + +
125D ARG* 3.2 30.7 - - - +
128D THR* 2.9 38.2 + - + +
130D PHE* 3.6 24.0 - + - -
145D GLN* 1.3 73.6 - - - +
147D ASN* 1.3 60.8 + - - +
148D VAL* 3.6 20.4 - - + +
150D PRO* 3.5 37.3 - - + +
151D GLN* 5.1 3.6 + - - +
----------------------------------------------------------
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