Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 4YXH
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 LEU 45 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H VAL* 3.9 17.5 - - + -
38H LYS 3.7 0.9 - - - -
39H GLN* 3.6 35.9 - - + +
44H GLY* 1.3 72.8 - - - -
46H GLU* 1.3 60.8 + - - +
95H PHE* 4.2 4.0 - - + -
109H TRP* 4.3 9.2 - - + -
36L TYR* 5.3 2.7 - - + -
38L GLN* 4.4 0.2 - - - +
44L PRO* 3.9 32.5 - - + -
87L TYR* 3.9 32.2 - - + -
98L PHE* 3.6 49.9 - - + +
99L GLY 5.0 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H VAL* 3.4 5.5 - - - +
38H LYS* 2.7 60.0 + - + +
40H ARG* 5.8 1.7 - - - +
44H GLY 5.2 1.1 - - - +
45H LEU* 1.3 74.3 - - - +
47H TRP* 1.3 72.9 + - - +
61H ASN* 3.9 6.9 + - - +
63H LYS* 3.8 28.2 + - - +
64H PHE* 3.9 23.1 - - + -
98L PHE* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP 3.5 13.5 - - - -
37H VAL* 4.6 1.3 - - + +
46H GLU* 1.3 76.3 - - - +
48H ILE* 1.3 63.3 - - - +
49H GLY* 3.2 13.7 - - - -
50H SER* 2.7 23.1 + - - -
59H SER* 3.4 23.8 - - - -
60H HIS 3.4 17.7 - - - -
61H ASN* 2.9 51.7 + - + +
64H PHE* 3.9 0.9 - - - -
106H MET* 4.6 8.7 - - + -
94L TRP* 3.4 32.1 - + + -
95L PRO* 3.5 28.3 - - + -
96L TYR* 3.4 47.5 - + + +
97L THR* 5.6 0.2 - - - -
98L PHE* 4.0 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 3.0 13.4 + - + +
37H VAL 4.1 4.0 - - - +
38H LYS* 3.5 23.3 - - + +
47H TRP* 1.3 75.3 - - - +
49H GLY* 1.3 59.1 + - - +
60H HIS* 3.5 4.1 - - + +
61H ASN* 2.7 30.4 + - - +
64H PHE* 3.7 37.3 - - + +
68H ALA* 3.7 29.4 - - + -
70H LEU* 5.4 1.6 - - + -
81H MET* 3.9 18.8 - - + -
83H LEU* 5.3 0.7 - - + -
94H TYR* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H HIS* 3.7 0.2 - - - -
36H TRP* 2.9 29.3 + - - +
47H TRP* 3.2 10.7 + - - +
48H ILE* 1.3 81.8 - - - +
50H SER* 1.3 64.5 + - - -
59H SER 3.1 14.4 - - - -
60H HIS* 4.0 2.2 - - - -
70H LEU* 3.4 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TRP* 3.8 17.5 - - - -
34H MET 3.2 5.4 - - - -
35H HIS* 2.7 33.9 + - - -
36H TRP* 5.2 0.2 - - - -
47H TRP* 2.7 31.0 + - - +
49H GLY* 1.3 73.3 + - - -
51H ILE* 1.3 62.0 + - - +
58H THR* 3.4 5.9 - - - +
59H SER 2.9 29.5 + - - +
70H LEU* 3.5 6.0 - - - +
94L TRP* 4.4 3.6 - - - -
96L TYR* 3.8 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TRP* 3.5 7.8 - - - -
34H MET* 2.9 51.7 + - + +
36H TRP* 5.0 8.5 - - - +
50H SER* 1.3 75.8 - - - +
52H ASP* 1.3 71.7 + - - +
53H PRO* 3.2 3.3 - - - +
56H SER* 3.7 23.1 - - - +
57H TYR 3.3 11.7 - - - +
58H THR* 3.8 10.1 - - + -
70H LEU* 3.7 31.6 - - + +
71H THR* 3.9 19.1 - - - +
72H VAL* 4.3 15.7 - - + -
79H ALA* 5.2 1.1 - - + -
----------------------------------------------------------
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