Contacts of the strand formed by residues 63 - 68 (chain B) in PDB entry 4NLH
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 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 6.3 1.3 - - - -
84A VAL* 4.0 30.1 - - + +
49B TRP* 3.9 17.0 - + + -
52B ILE 4.0 1.6 - - - +
53B PHE* 3.5 27.5 - - + -
60B ALA 3.6 15.0 - - - -
61B ARG* 3.2 15.1 + - - +
62B ASP* 1.3 80.2 - - - +
64B TYR* 1.3 60.9 + - - +
65B THR* 3.7 30.7 - - - +
66B PHE* 3.7 32.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 5.9 0.8 - - + +
21A ASN* 3.3 29.5 + - - +
33A GLU* 3.9 3.1 - - - +
35A HIS* 3.1 66.5 + + + +
84A VAL* 4.0 6.6 - - - +
52B ILE* 2.8 20.0 + - + +
53B PHE* 4.7 0.9 - - - +
54B LYS* 5.3 1.1 - - + +
62B ASP 3.9 0.6 + - - -
63B TYR* 1.3 76.7 - - - +
65B THR* 1.3 64.3 + - + +
91B TYR 3.5 22.0 - - - -
92B LEU 3.8 0.9 - - - -
93B PRO* 3.5 32.2 - - + +
94B ASN* 4.9 0.5 + - - -
96B ASP* 5.4 0.8 + - - -
100B TYR* 4.0 32.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.7 33.9 + - - -
51B GLY* 3.5 1.7 - - - -
52B ILE* 2.9 43.4 + - + +
63B TYR* 3.8 11.1 - - - -
64B TYR* 1.3 78.2 - - + +
66B PHE* 1.3 73.2 + - - +
87B PHE* 4.1 21.1 - - + -
91B TYR* 3.6 30.5 - - + +
92B LEU* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 4.9 6.5 + - - +
49B TRP* 3.5 37.9 - + + -
50B VAL 3.3 7.2 - - - +
63B TYR* 3.7 33.0 - + + -
65B THR* 1.3 83.3 + - - +
67B LEU* 1.3 83.1 + - - +
68B TRP* 3.6 51.8 - + - -
87B PHE* 4.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 3.3 1.6 - - - +
50B VAL* 2.9 31.3 + - - +
66B PHE* 1.3 87.9 - - - +
68B TRP* 1.3 65.2 + - - +
85B LEU* 4.2 22.6 - - + +
86B ALA 3.3 31.4 - - - +
87B PHE* 3.7 33.4 - - + -
88B GLN* 6.6 0.4 - - + -
91B TYR* 6.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO 4.9 5.6 - - - +
47B LYS* 3.2 45.8 - - + -
48B ASP 3.6 6.3 - - - +
49B TRP* 3.8 17.5 - + + -
66B PHE* 3.6 28.7 - + - -
67B LEU* 1.3 75.1 - - - +
69B SER* 1.3 62.3 + - - +
70B PRO* 3.1 14.4 - - + +
85B LEU* 3.7 11.0 - - - +
----------------------------------------------------------
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