Contacts of the strand formed by residues 120 - 125 (chain D) in PDB entry 4JRY
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 THR 120 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 3.6 18.1 + - - +
7D ASN 4.2 4.3 + - - -
8D PRO* 2.8 30.0 + - + +
9D LEU 3.3 4.5 - - - +
11D LEU* 4.6 1.3 - - + -
21D ILE* 3.6 37.5 - - + +
22D TYR 5.0 0.3 + - - -
100D ALA 3.7 0.3 - - - +
101D THR* 3.9 2.3 - - - +
102D TYR* 2.9 37.0 + - - +
119D GLY* 1.3 72.9 + - - -
121D LYS* 1.3 65.6 + - - +
122D LEU* 3.4 13.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU 2.9 13.6 + - - +
10D PHE* 3.2 9.9 - - + +
11D LEU 2.8 31.2 + - - +
100D ALA 3.6 8.1 - - - +
101D THR* 4.1 19.3 - - + +
119D GLY 4.1 0.4 - - - -
120D THR* 1.3 68.5 - - - +
122D LEU* 1.3 59.6 + - - +
123D ILE* 3.8 29.0 + - + +
187E GLN* 3.7 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.8 9.9 - - + -
13D MET* 3.6 28.0 - - + -
21D ILE* 4.1 12.8 - - + -
91D ILE* 3.7 31.0 - - + -
98D LEU 4.1 6.5 - - - +
99D SER* 3.2 22.2 - - - -
100D ALA 2.7 20.3 + - - +
102D TYR* 3.5 31.0 - - + -
120D THR* 3.4 26.6 + - + +
121D LYS* 1.3 72.0 - - - +
123D ILE* 1.3 63.5 + - - +
124D ILE* 3.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PHE* 3.4 34.5 - - + -
11D LEU 2.8 12.4 + - - +
12D SER* 3.6 8.1 + - - +
13D MET* 2.9 30.7 + - - +
99D SER* 4.1 2.2 - - - -
121D LYS* 3.8 27.8 - - + +
122D LEU* 1.3 75.6 - - - +
124D ILE* 1.4 59.3 + - - +
125D LYS* 3.6 21.9 + - + +
173D LYS* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D MET* 3.4 40.4 - - + +
15D GLU* 3.7 29.6 - - + +
94D ALA* 3.7 8.7 - - + -
95D VAL* 3.5 37.2 - - - +
96D HIS* 3.0 33.9 - - + +
98D LEU* 3.8 12.6 - - + +
99D SER* 2.9 36.2 + - - +
122D LEU* 4.2 7.6 - - + -
123D ILE* 1.4 71.7 - - - +
125D LYS* 1.3 60.2 - - - +
175D VAL* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER* 3.2 25.9 + - - +
13D MET 2.8 13.6 + - - +
14D GLN* 3.5 26.3 - - - +
15D GLU* 2.9 27.9 + - - +
96D HIS* 5.9 0.2 - - - -
123D ILE* 4.2 18.4 - - + +
124D ILE* 1.3 73.9 - - - +
126D PRO* 1.3 70.7 - - + +
156D SER* 3.6 23.8 + - - +
157D GLN* 4.9 7.0 - - + +
159D ASN* 4.6 7.5 + - - -
173D LYS* 3.5 29.7 - - - +
175D VAL* 5.2 0.7 - - + -
----------------------------------------------------------
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