Contacts of the strand formed by residues 49 - 54 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 3.3 18.8 + - - -
48A ASP* 1.3 75.1 - - - +
50A VAL* 1.3 63.4 + - - +
51A GLY* 3.8 14.4 - - - -
53A PHE* 3.8 14.8 - + - -
60A ALA* 3.3 29.8 - - + -
63A TYR* 4.1 12.6 - + + -
66A PHE* 3.5 40.4 - + + -
67A LEU 3.1 19.7 - - - +
68A TRP* 4.0 15.2 - + + -
69A SER* 3.7 4.3 - - - +
103A CYS 3.7 0.3 - - - +
104A TYR* 3.5 4.4 - - - -
105A VAL* 2.8 78.4 + - + +
106A THR 4.3 3.4 + - - -
107A HIS* 5.7 0.2 - - - +
109A GLY* 5.8 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.8 25.1 - - + -
34A CYS* 4.1 9.9 - - - -
36A TYR* 3.9 15.5 - - + +
49A TRP* 1.3 79.6 - - - +
51A GLY* 1.3 68.2 + - - +
66A PHE* 3.3 1.4 - - - -
67A LEU 3.0 29.9 + - - -
69A SER* 4.6 1.5 - - - +
85A LEU* 3.8 23.6 - - + -
87A PHE* 3.6 17.2 - - + -
102A PHE* 4.4 2.7 - - + -
103A CYS 3.2 7.9 - - - +
104A TYR* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TRP* 3.8 5.3 - - - -
50A VAL* 1.3 77.9 - - - +
52A ILE* 1.3 65.6 + - - +
53A PHE* 3.6 17.5 - - - -
63A TYR* 4.8 0.7 - - - -
65A THR 3.3 9.0 - - - -
66A PHE* 3.9 7.6 - - - -
102A PHE* 3.3 5.9 - - - -
103A CYS 2.9 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.5 0.9 - - + -
51A GLY* 1.3 71.8 - - - -
53A PHE* 1.3 55.7 + - - +
63A TYR* 3.6 0.7 - - - -
64A TYR* 2.6 40.5 + - + +
65A THR* 2.8 21.5 + - + +
87A PHE* 4.0 23.8 - - + -
92A LEU* 3.5 32.1 - - + -
93A PRO* 4.7 4.0 - - + -
100A TYR* 4.0 29.4 - - + -
101A GLN 3.5 4.7 - - - +
102A PHE* 3.7 32.8 - - + -
118A PHE* 4.7 1.6 - - + -
120A PHE* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TRP* 3.8 12.6 - + - -
51A GLY* 3.6 28.5 - - - -
52A ILE* 1.3 78.8 - - - +
54A LYS* 1.3 61.8 + - - +
57A TRP* 3.6 35.4 - + + -
59A THR 3.7 13.2 - - - -
60A ALA* 3.7 20.2 - - - -
62A ASP 3.7 4.7 - - - -
63A TYR* 3.3 36.6 - - + +
64A TYR 4.4 2.2 - - - +
100A TYR* 3.2 6.0 - - - -
101A GLN* 2.8 35.4 + - + +
103A CYS* 3.7 30.1 - - + -
105A VAL* 4.2 5.2 - - + -
111A ILE* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 1.3 72.4 - - - +
55A VAL* 1.3 77.5 + - - +
57A TRP* 3.2 22.2 + - - +
62A ASP 4.6 8.0 + - - +
64A TYR* 5.0 2.7 - - + +
98A GLU* 3.2 38.3 + - + +
99A PHE 3.5 12.8 - - - +
100A TYR* 3.5 20.6 - - + +
----------------------------------------------------------
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