Contacts of the strand formed by residues 49 - 54 (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 TRP 49 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS 3.2 18.2 - - - -
48B ASP* 1.3 76.6 - - - +
50B VAL* 1.3 64.8 + - - +
51B GLY* 3.9 15.0 - - - -
53B PHE* 3.7 12.8 - + - -
60B ALA* 3.4 30.1 - - + -
63B TYR* 3.9 15.5 - + - -
66B PHE* 3.5 35.2 - + + -
67B LEU 3.3 14.8 - - - +
68B TRP* 3.8 20.8 - + + -
69B SER* 3.6 4.7 - - - +
104B TYR* 3.7 4.2 - - - -
105B VAL* 2.8 81.1 + - + +
106B THR 4.0 5.3 + - - -
107B HIS* 5.6 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 4.1 18.8 - - + -
34B CYS* 4.2 11.0 - - - -
36B TYR* 3.9 19.1 - - + +
49B TRP* 1.3 80.8 - - - +
51B GLY* 1.3 67.2 + - - +
66B PHE* 3.3 2.3 - - - -
67B LEU 2.9 31.1 + - - -
69B SER* 4.4 1.8 - - - -
85B LEU* 3.7 26.2 - - + -
87B PHE* 3.6 18.4 - - + -
102B PHE* 4.3 2.2 - - + -
103B CYS 3.4 9.0 - - - +
104B TYR* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 3.9 11.7 - - - -
50B VAL* 1.3 77.7 - - - +
52B ILE* 1.3 65.4 + - - -
53B PHE* 3.6 18.0 - - - -
63B TYR* 4.8 0.4 - - - -
65B THR 3.5 8.7 - - - -
102B PHE* 3.4 8.7 - - - -
103B CYS 3.0 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.6 1.8 - - + -
51B GLY* 1.3 72.8 - - - -
53B PHE* 1.3 60.0 + - - +
63B TYR 3.9 0.3 - - - -
64B TYR* 2.8 35.3 + - + +
65B THR* 2.9 19.9 + - + +
87B PHE* 4.0 22.0 - - + -
92B LEU* 3.6 31.2 - - + -
93B PRO* 4.8 3.6 - - + -
100B TYR* 4.0 30.1 - - + -
101B GLN 3.5 5.2 - - - +
102B PHE* 3.7 28.5 - - + -
118B PHE* 4.6 2.9 - - + -
120B PHE* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 3.7 16.8 - + - -
51B GLY* 3.6 25.4 - - - -
52B ILE* 1.3 73.7 - - - +
54B LYS* 1.3 60.1 + - - +
55B VAL 3.6 0.2 + - - -
57B TRP* 3.5 35.0 - + + +
59B THR 3.9 4.9 - - - -
60B ALA* 3.4 34.3 - - - -
62B ASP 3.5 19.3 - - - -
63B TYR* 3.5 13.7 - - + -
100B TYR* 3.1 5.0 - - - -
101B GLN* 2.7 44.3 + - + +
103B CYS* 3.5 35.9 - - + -
105B VAL* 4.2 6.5 - - + -
111B ILE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 3.2 30.1 - - - +
52B ILE 4.3 0.4 + - - -
53B PHE* 1.3 71.6 - - - +
55B VAL* 1.3 79.2 + - + +
57B TRP* 2.9 23.1 + - - +
62B ASP 4.8 5.6 + - - +
64B TYR* 5.3 1.4 - - - +
98B GLU* 3.9 37.4 + - + +
99B PHE 3.4 13.9 - - - +
100B TYR* 3.5 23.9 - - + +
----------------------------------------------------------
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