Contacts of the strand formed by residues 52 - 57 (chain B) in PDB entry 4PH8
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 52 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY 3.6 3.1 + - - +
51B ALA* 1.3 73.6 - - - +
53B VAL* 1.3 67.6 + - - +
54B TRP* 3.4 40.3 - - + +
98B TYR* 3.9 27.7 - - + -
99B LYS 3.4 15.5 - - - +
100B LYS* 4.3 10.5 - - + +
134B VAL* 3.3 1.9 - - - -
135B ASP* 2.8 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.9 22.7 - - + +
41B THR 4.2 8.7 - - - +
42B THR* 4.6 0.7 - - + -
51B ALA 4.3 0.2 + - - -
52B LYS* 1.3 74.6 - - - +
54B TRP* 1.3 64.3 + - - +
98B TYR* 3.1 7.8 - - - +
99B LYS 2.9 41.6 + - - +
101B LEU* 3.8 30.7 - - + -
108B LEU* 3.7 29.5 - - + +
133B ALA 3.2 11.0 - - - +
134B VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.0 4.2 - - - +
52B LYS* 3.4 42.7 - - + +
53B VAL* 1.3 79.3 - - - +
55B LEU* 1.3 63.1 + - - +
56B TRP* 3.9 17.5 - - + -
89B VAL* 3.5 29.2 - - + -
96B LYS* 3.6 21.3 - - + -
97B ILE 3.1 18.2 - - - -
98B TYR* 3.7 17.7 - + + -
108B LEU* 4.1 4.0 - - - -
132B ALA* 3.1 9.8 - - - +
133B ALA* 2.8 34.2 + - + +
135B ASP* 2.8 29.8 + - - -
201B GOL 3.6 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.9 19.1 - - + -
38B ALA* 3.9 21.3 - - + +
40B VAL* 3.7 24.0 - - + -
54B TRP* 1.3 74.8 - - - +
56B TRP* 1.3 65.1 + - - +
64B TRP* 3.9 15.0 - - + -
96B LYS* 4.2 0.3 - - - +
97B ILE* 2.9 41.4 + - + +
108B LEU* 4.1 14.8 - - + +
110B ALA* 3.6 32.5 - - + +
130B LEU* 4.5 7.4 - - + -
131B HIS 3.3 16.2 - - - +
132B ALA* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B TRP* 3.9 11.0 - - + -
55B LEU* 1.3 86.9 - - - +
57B GLY* 1.3 76.3 - - - +
62B ASN* 3.7 23.3 - - + -
64B TRP* 4.3 8.3 - - - +
95B ALA 5.4 0.4 - - - -
96B LYS* 3.6 36.4 - - + +
130B LEU* 3.6 4.5 - - - +
131B HIS* 2.8 74.2 + + + +
132B ALA* 3.8 13.5 - - - -
133B ALA* 3.8 26.7 - - + -
146B GLN* 3.8 23.1 - - - -
201B GOL 3.8 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 1.3 90.8 - - - +
58B THR* 1.3 62.1 + - - +
59B GLY 3.5 0.2 - - - -
62B ASN* 3.0 23.7 + - - +
63B LYS 3.4 16.8 - - - -
64B TRP* 3.7 13.4 - - - -
129B ILE 4.0 11.0 - - - -
130B LEU* 4.3 1.1 - - - -
131B HIS* 4.7 1.0 - - - -
----------------------------------------------------------
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