Contacts of the strand formed by residues 43 - 49 (chain D) in PDB entry 3HN3
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 43 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TRP* 3.5 34.6 - - - -
42D ASP* 1.3 76.1 - - - +
44D LEU* 1.3 65.6 + - - -
45D TRP* 3.6 3.8 - - - -
78D PRO* 3.5 4.1 - - - +
79D VAL 2.8 35.4 + - - +
103D ARG* 3.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TRP* 3.4 42.9 - - + -
367A VAL* 3.5 26.9 - - + -
395A MET* 4.0 10.8 - - + -
398A ARG* 3.9 25.6 - - - +
43D GLY* 1.3 72.3 - - - -
45D TRP* 1.3 61.2 + - - +
76D ASP* 4.2 20.0 - - + +
77D MET 3.8 1.6 - - - +
78D PRO* 4.8 5.2 - - + -
103D ARG* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 2.9 30.2 + - + -
43D GLY 3.6 3.6 - - - -
44D LEU* 1.3 82.0 - - - +
46D SER* 1.3 64.6 + - - +
76D ASP* 3.5 6.5 - - - -
77D MET* 2.9 37.3 + - - +
79D VAL* 3.2 33.2 - - + +
101D TYR* 4.0 13.7 - - + -
102D GLU* 3.5 20.6 - - - -
103D ARG* 3.5 37.5 - - + +
168D ILE* 4.0 20.9 - - + -
170D ILE* 4.0 30.3 - - + -
214D LEU* 4.3 3.4 - - + -
218D VAL* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D TRP* 1.3 75.2 - - - +
47D PHE* 1.3 59.0 + - - +
68D LEU* 4.1 12.1 - - - +
69D TRP* 5.9 1.7 - - - +
74D THR* 4.6 13.6 + - - -
75D VAL 3.6 5.8 - - - -
76D ASP* 5.0 2.1 + - - +
101D TYR* 3.2 6.9 - - - +
102D GLU* 2.7 47.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D SER* 1.3 77.2 - - - +
48D ARG* 1.3 60.9 + - - +
49D ALA* 3.8 13.9 - - + -
68D LEU* 4.2 3.9 - - - +
74D THR* 3.4 6.5 - - - -
75D VAL* 2.8 45.1 + - + +
77D MET* 3.5 37.9 - - + -
83D PHE* 3.8 23.1 - + + -
92D LEU* 4.0 15.9 - - + -
99D VAL* 3.7 31.2 - - + -
100D TRP 3.2 10.3 - - - -
101D TYR* 3.6 43.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 1.3 82.1 - - - +
49D ALA* 1.3 73.7 + - - +
50D ASP* 5.7 0.6 + - - +
57D ARG* 5.4 6.1 - - - +
61D GLU* 5.4 1.0 + - - -
63D TRP* 3.1 50.5 - - + -
68D LEU* 4.4 15.0 + - + -
71D SER* 2.9 36.4 + - - -
72D GLY* 3.8 7.0 - - - +
73D PRO* 3.5 25.5 + - - +
74D THR* 4.5 4.5 - - + -
99D VAL* 3.7 0.3 - - - -
100D TRP* 2.8 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PHE* 3.8 5.4 - - + -
48D ARG* 1.3 87.9 + - - +
50D ASP* 1.3 58.8 + - - +
51D PHE* 3.4 46.5 + - + -
63D TRP* 5.1 0.2 - - - -
92D LEU* 3.8 20.4 - - + -
95D PHE* 4.2 4.7 - - + -
98D TRP 4.0 4.5 - - - -
99D VAL* 4.1 13.0 - - + -
----------------------------------------------------------
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