Contacts of the strand formed by residues 68 - 75 (chain D) in PDB entry 4J1R
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 GLY 68 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C TYR* 4.6 0.6 + - - -
64D ASN* 3.6 7.1 - - - +
65D GLY 3.0 31.7 + - - +
66D SER 3.5 0.4 - - - -
67D PHE* 1.3 86.0 - - - +
69D VAL* 1.3 66.7 + - - -
86D LYS 3.4 6.5 - - - -
88D LEU 5.6 0.2 - - - -
127D TYR* 6.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C TYR* 3.2 38.4 - - + -
61D VAL* 3.6 20.6 - - + -
63D GLY 3.4 13.9 - - - +
67D PHE* 3.9 1.3 - - - -
68D GLY* 1.3 79.9 - - - -
70D VAL* 1.3 65.9 + - - +
71D TYR* 3.8 31.6 - - + +
84D ILE 3.6 0.3 - - - +
85D LYS* 3.5 2.3 - - - -
86D LYS* 2.7 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D VAL* 3.7 2.9 - - - +
62D ILE* 2.7 46.8 + - + +
63D GLY* 3.0 21.3 + - - +
67D PHE* 3.6 20.4 - - + -
69D VAL* 1.3 80.9 - - - +
71D TYR* 1.3 61.9 + - - +
83D ALA* 4.3 10.3 - - + -
84D ILE 3.3 7.9 - - - +
85D LYS* 4.1 11.2 - - + +
502D I5R 3.4 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C TYR* 4.4 11.2 - - + +
59D THR* 3.5 30.7 - - + -
60D LYS* 3.3 5.6 - - - -
61D VAL* 3.6 32.3 - - + -
62D ILE* 3.9 2.8 - - - +
69D VAL* 3.8 31.1 - - + +
70D VAL* 1.3 76.5 - - - +
72D GLN* 1.3 62.9 + - - +
73D ALA 4.2 0.2 - - - -
83D ALA* 3.2 8.7 - - - +
84D ILE* 2.8 55.4 + - + +
86D LYS* 4.0 30.0 + - + +
129D ASN* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ASP* 3.0 22.2 - - - +
59D THR* 3.3 1.3 - - - -
60D LYS* 2.8 46.2 + - + +
62D ILE* 3.5 24.9 - - + -
71D TYR* 1.3 75.5 - - - +
73D ALA* 1.3 63.5 + - - +
81D LEU* 3.3 43.6 - - - +
82D VAL 3.5 4.7 - - - +
134D TYR* 3.5 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 3.5 35.2 - - + -
57D THR 3.6 8.3 - - - +
58D ASP 3.8 2.5 - - - -
59D THR* 3.8 5.8 - - - +
71D TYR 4.2 0.4 - - - -
72D GLN* 1.3 76.9 + - - +
74D LYS* 1.3 62.7 + - - +
81D LEU* 3.4 11.0 - - - +
82D VAL* 3.0 35.7 + - + +
84D ILE* 4.0 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D TYR* 3.2 4.0 - - - -
57D THR* 2.8 56.1 + - - +
58D ASP* 3.6 24.3 + - + +
73D ALA* 1.3 74.2 - - - +
75D LEU* 1.3 68.2 + - - +
76D CYS* 3.4 2.5 + - - +
79D GLY* 3.1 35.9 - - - +
80D GLU 3.4 3.4 - - - +
81D LEU* 3.7 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 4.2 17.5 - - + -
55D SER 3.5 12.1 - - - +
56D TYR* 4.2 9.2 - - + -
73D ALA 4.3 0.2 - - - -
74D LYS* 1.3 72.4 - - - +
76D CYS* 1.3 58.7 + - - +
77D ASP* 3.5 15.3 - - - +
78D SER* 3.4 24.0 - - - +
79D GLY* 2.8 32.4 + - - -
80D GLU 2.9 16.5 + - - +
82D VAL* 4.0 30.3 - - + -
113D ARG* 3.8 21.1 - - - +
114D TYR* 4.3 18.8 - - + +
131D VAL* 5.2 3.4 - - + -
----------------------------------------------------------
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