Contacts of the strand formed by residues 76 - 81 (chain D) in PDB entry 4LL4
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 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL 3.5 0.9 - - - +
26D ASP 3.8 0.3 - - - -
27D PHE* 2.8 40.4 + - - +
71D VAL* 4.0 18.6 - - + +
72D LYS 4.8 1.3 + - - +
73D CYS* 2.9 26.7 + - - -
74D MET* 3.6 2.0 - - - +
75D PRO* 1.3 71.0 - - - +
77D PHE* 1.3 63.4 + - - +
78D GLN* 4.2 9.9 - - + +
88D GLU* 3.5 27.4 - - + +
89D PHE 3.8 6.1 - - - +
90D SER* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.3 2.2 - - + -
25D VAL 3.3 2.5 - - - -
26D ASP* 3.3 43.1 - - + -
38D ILE* 4.2 24.5 - - + -
42D PHE* 3.5 27.8 - + - -
75D PRO* 3.8 22.0 - - + -
76D THR* 1.3 73.9 - - - +
78D GLN* 1.3 63.6 + - - +
79D PHE* 3.8 10.1 - - + -
88D GLU* 3.2 7.3 - - - +
89D PHE* 2.9 68.3 + + + +
91D GLY 3.9 13.2 - - - -
97D LEU* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL 3.6 0.9 - - - +
24D VAL* 3.5 5.0 - - - +
25D VAL* 2.9 33.6 + - + +
27D PHE* 3.4 28.7 - - + -
69D CYS* 3.3 33.3 + - - +
71D VAL* 4.4 5.7 - - - +
76D THR* 4.2 3.4 - - + -
77D PHE* 1.3 77.9 - - - +
79D PHE* 1.3 64.2 + - - +
80D PHE* 3.6 26.1 - - + -
85D LYS* 3.3 14.7 + - + +
87D GLY 3.6 5.4 - - - +
88D GLU* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.0 19.3 - - + -
23D VAL 3.3 1.8 - - - -
24D VAL* 3.8 30.7 - - + -
77D PHE* 3.8 22.7 - - + -
78D GLN* 1.3 77.2 - - - +
80D PHE* 1.3 62.5 + - - +
85D LYS* 3.3 6.3 - - - +
86D VAL* 2.8 35.0 + - + -
87D GLY* 3.0 35.8 + - - +
88D GLU 3.8 1.3 - - - -
89D PHE* 4.2 14.4 - + - -
97D LEU* 4.6 7.4 - - + -
100D THR* 3.6 35.0 - - + -
101D ILE* 4.1 17.9 - - + -
104D LEU* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 4.5 15.5 - + - -
15D LEU* 4.6 20.2 - - + -
22D LEU* 3.6 6.6 - - - +
23D VAL* 2.9 45.8 + - + -
25D VAL* 3.7 25.6 - - + -
69D CYS* 4.8 5.6 - - - -
78D GLN* 3.6 39.7 - - + -
79D PHE* 1.3 79.6 - - - +
81D LYS* 1.3 70.4 + - - +
83D GLY 4.2 7.9 - - - +
84D GLN 3.4 26.7 - - - +
85D LYS* 3.7 19.3 - - + -
86D VAL* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ASP* 3.4 27.4 + - - +
21D LYS 4.2 7.6 - - - +
22D LEU* 4.6 6.1 - - - +
23D VAL* 4.8 1.3 - - - +
80D PHE* 1.3 82.0 - - - +
82D LYS* 1.3 75.2 + - + +
83D GLY 3.1 0.9 - - - -
84D GLN* 2.9 25.2 + - - +
86D VAL* 4.4 22.4 - - + -
104D LEU* 3.2 27.8 - - - +
105D VAL* 3.2 15.5 + - - -
----------------------------------------------------------
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