Contacts of the strand formed by residues 87 - 94 (chain H) in PDB entry 4NQD
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 SER 87 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ARG* 3.5 23.9 + - - +
37H GLN 3.1 6.9 + - - -
38H ASP* 2.6 26.3 + - - -
85H GLN 3.2 3.5 + - - -
86H THR* 1.3 77.6 - - - +
88H VAL* 1.3 69.8 + - - +
89H TYR* 3.7 19.5 - - - -
110H SER 3.6 1.0 - - - +
111H ARG* 3.8 2.3 - - - +
112H LEU 3.0 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ARG* 3.4 2.3 - - - -
37H GLN* 2.8 45.5 + - + +
87H SER* 1.3 80.3 + - - +
89H TYR* 1.3 66.4 + - - +
90H PHE* 3.6 28.7 + - + -
110H SER 3.4 6.3 - - - +
111H ARG* 3.7 45.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 2.6 24.4 + - - -
21H LEU* 3.8 12.3 - - + -
34H TRP* 3.7 15.5 - - + -
35H TYR 3.4 4.9 - - - -
36H ARG* 3.9 7.0 - - + -
46H ILE* 3.7 23.8 - - + -
64H TYR* 2.6 45.5 + + - -
76H LEU* 3.8 10.8 - - + -
78H LEU* 4.1 1.8 - - + +
85H GLN* 2.5 32.8 + - - +
87H SER* 3.7 17.9 - - - -
88H VAL* 1.3 72.8 - - - +
90H PHE* 1.3 56.6 + - - +
109H GLY* 3.2 3.5 - - - -
110H SER 2.8 31.3 + - - +
112H LEU* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G GLN* 3.6 17.9 - - - -
41G GLU 3.7 6.7 - - - -
42G ALA* 3.7 11.7 - - - -
43G PRO* 4.3 8.5 - - + -
6H GLN* 3.8 0.7 - - - -
33H TYR 3.8 0.5 - - - +
34H TRP* 3.5 5.5 - - - -
35H TYR* 2.7 46.9 + - + +
37H GLN* 3.4 30.7 - - + -
43H LEU* 4.6 8.1 - - + -
88H VAL* 3.6 28.9 - - + -
89H TYR* 1.3 74.6 - - - +
91H CYS* 1.3 60.5 + - - +
92H ALA 4.0 0.2 + - - -
106H PHE* 3.9 21.3 - + + -
107H GLY 3.3 21.5 - - - -
108H GLU 3.6 8.7 - - - -
109H GLY* 3.5 20.6 - - - -
111H ARG* 4.1 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.2 2.9 - - + -
6H GLN* 3.2 14.9 + - + +
23H CYS* 2.0 52.9 - - + -
32H MET* 4.1 8.3 - - - -
33H TYR 3.3 11.2 - - - -
34H TRP* 3.8 22.2 - - + -
74H PHE* 4.9 1.8 - - - -
90H PHE* 1.3 74.9 - - - +
92H ALA* 1.3 66.1 + - - +
106H PHE* 3.5 3.3 - - - +
107H GLY 2.7 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.9 1.6 - - - -
32H MET* 3.4 4.7 - - - +
33H TYR* 2.8 49.1 + - + +
35H TYR* 4.6 2.2 - - + -
90H PHE 4.0 0.4 + - - -
91H CYS* 1.3 80.8 - - - +
93H SER* 1.3 60.0 + - - +
104H LEU* 4.3 13.2 - - + -
105H PHE 3.1 13.2 - - - +
106H PHE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 3.5 19.3 - - - +
25H GLN* 3.9 23.4 - - - +
27H MET* 4.6 0.3 - - - -
29H HIS* 2.7 27.7 + - - -
31H SER 3.3 13.5 - - - -
32H MET* 4.3 4.3 - - - -
33H TYR* 4.2 4.5 - - - -
92H ALA* 1.3 75.3 - - - +
94H SER* 1.3 61.2 + - - +
104H LEU* 3.6 1.9 - - - -
105H PHE* 2.8 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H HIS* 3.1 21.4 - - - +
31H SER* 3.1 17.5 + - - -
33H TYR* 2.6 29.9 + - - -
93H SER* 1.3 72.8 - - - +
95H VAL* 1.4 65.3 + - - +
96H TRP 2.9 17.9 + - - -
102H GLY* 4.7 7.9 - - - -
103H GLU 3.4 22.7 - - - -
104H LEU* 3.9 7.6 - - - -
105H PHE* 4.9 0.2 - - - -
----------------------------------------------------------
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