Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 4JHN
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 ARG 127 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP 3.6 5.4 - - - +
65A GLY 3.6 0.5 - - - +
111A THR* 3.7 4.0 - - - +
112A GLY* 2.9 31.8 + - - +
114A ASN* 3.9 2.4 - - - +
119A LEU* 3.6 17.7 - - + -
121A LEU* 3.6 27.3 + - + +
123A ASP* 2.9 36.3 + - - -
125A GLU* 2.6 36.4 + - - +
126A GLU* 1.3 80.0 - - - +
128A ASN* 1.3 59.3 + - - +
129A THR 3.6 16.2 - - - +
131A HIS* 3.6 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP 5.2 0.4 - - - +
65A GLY* 3.7 15.0 - - - -
68A GLY* 3.1 8.4 + - - -
69A LEU 3.2 0.5 + - - -
70A GLY* 2.9 55.8 + - - +
71A SER* 3.7 12.7 + - - -
111A THR* 3.4 7.6 - - - -
127A ARG* 1.3 73.3 - - - +
129A THR* 1.3 70.3 + - - +
131A HIS* 5.4 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.7 13.9 - - - +
69A LEU 5.1 0.9 - - - -
70A GLY* 4.4 7.4 - - - +
110A ALA 3.8 1.0 - - - +
111A THR* 3.3 13.0 + - - -
127A ARG* 3.8 2.8 - - - +
128A ASN* 1.3 94.3 + - - +
130A PHE* 1.3 62.5 + - - +
131A HIS* 2.8 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.8 28.0 - - + -
58A MET* 4.7 2.2 - - - -
67A LEU 3.8 21.3 - - - -
68A GLY* 4.0 7.4 + - - -
81A VAL* 3.8 22.4 - - + -
83A ALA* 6.4 2.2 - - + +
84A LEU* 3.9 13.2 - - + -
99A THR* 3.9 22.0 - - + -
101A VAL* 3.6 19.7 - - + -
109A TYR* 3.8 36.6 - - + -
110A ALA* 3.5 9.4 - - - -
111A THR* 3.5 23.6 - - + -
129A THR* 1.3 76.1 + - - +
131A HIS* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.2 5.6 - - - -
110A ALA 2.9 29.2 + - - +
121A LEU* 3.8 25.1 - - + +
127A ARG* 3.6 42.5 + - + +
128A ASN 5.4 0.7 - - - -
129A THR* 2.8 43.2 + - - -
130A PHE* 1.3 75.0 - - - +
132A VAL* 1.3 64.8 + - - +
133A ILE 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 4.3 18.6 - - + +
108A VAL 3.5 4.3 - - - +
109A TYR* 3.3 36.6 - - + +
121A LEU* 3.3 13.3 - - - +
131A HIS* 1.3 72.5 - - - +
133A ILE* 1.3 62.1 + - - +
134A SER* 3.3 13.4 + - - +
----------------------------------------------------------
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