Contacts of the strand formed by residues 93 - 100 (chain D) in PDB entry 2Q2U
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 PHE 93 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 5.8 0.4 - - + -
52D MET* 3.6 53.4 - - + -
55D LEU* 4.3 10.1 - - + -
56D LEU* 4.3 15.9 - - + -
68D ILE* 4.1 4.5 - - + -
69D SER 4.2 2.5 - - - +
70D ILE* 3.3 27.1 - - + +
71D GLU* 5.2 1.8 - - - +
89D TYR* 4.2 4.0 - + + -
91D ALA 4.0 9.0 - - - -
92D LYS* 1.3 82.4 - - - +
94D SER* 1.3 73.4 + - - +
95D TYR* 5.4 0.4 - - + -
131D GLN* 3.5 11.0 + - + +
132D VAL* 3.2 48.5 - - + -
133D LYS* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 3.6 4.2 - - - -
69D SER 3.0 34.3 + - - -
70D ILE* 4.8 0.2 - - - +
71D GLU* 3.1 39.8 + - - +
93D PHE* 1.3 83.2 - - - +
95D TYR* 1.3 62.2 + - - +
96D TYR* 4.3 4.0 - - - -
132D VAL* 5.2 0.2 - - - -
133D LYS* 3.2 23.8 - - - +
135D ILE* 3.7 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 2.7 28.6 + - - -
39D MET* 3.9 13.1 - - + +
56D LEU* 3.8 25.8 - - + -
60D LEU* 3.4 35.2 - - + +
64D SER 3.5 9.0 + - - -
65D ASP 3.3 3.8 - - - -
66D GLY* 2.9 26.3 + - - -
67D GLU 3.3 10.5 - - - -
68D ILE* 3.8 20.9 - - + -
93D PHE* 5.4 0.7 - - + -
94D SER* 1.3 74.7 - - - +
96D TYR* 1.3 60.0 + - - +
97D TRP* 3.2 24.7 + + + -
132D VAL* 4.8 2.9 - - + -
133D LYS 3.0 9.1 + - - +
134D ILE* 3.6 7.4 - - + +
135D ILE* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE* 3.5 36.8 - - + -
66D GLY* 2.9 26.0 - - - -
67D GLU* 2.8 23.5 + - + +
69D SER* 4.3 15.5 - - - -
71D GLU* 2.6 34.5 + - - -
94D SER* 4.3 2.0 - - - -
95D TYR* 1.3 75.0 - - - +
97D TRP* 1.3 60.4 + - - +
98D PHE* 3.4 4.8 + - + -
135D ILE* 3.2 36.6 - - + +
137D LEU* 3.6 36.3 - - + -
160D PHE* 4.3 20.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D LEU* 4.1 8.3 - - + -
61D PRO* 3.7 24.7 - - + -
64D SER* 3.0 34.2 + - - +
65D ASP 3.3 11.0 - - - -
95D TYR* 3.2 15.1 + + + -
96D TYR* 1.3 68.9 - - - +
98D PHE* 1.3 59.4 + - - +
99D ASP 2.8 28.3 + - - -
100D TYR* 3.8 12.3 - + - -
116D MET* 3.2 42.5 - - + +
119D TYR* 3.8 13.5 - + + -
120D ILE* 4.1 22.9 - - + -
126D ILE* 4.2 13.0 - - + -
134D ILE* 4.3 20.0 - - + -
135D ILE 2.7 11.4 + - - +
136D PRO* 4.3 4.9 - - + -
137D LEU 2.7 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D THR* 5.3 4.0 - - - +
28D ILE* 5.8 1.8 - - + -
32D ARG* 3.4 28.0 - - - -
65D ASP* 3.0 31.4 + - - -
66D GLY* 3.3 21.5 - - - -
67D GLU* 3.9 13.5 - - + -
96D TYR* 3.6 14.6 - - + -
97D TRP* 1.3 74.2 - - - +
99D ASP* 1.3 64.6 + - + +
109D TYR* 3.8 25.6 + - - +
113D VAL* 5.3 2.3 - - - +
116D MET* 4.2 7.0 - - - +
137D LEU* 3.9 34.5 - - + +
166D ARG* 3.5 24.0 + - - +
184D LEU* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU* 4.2 1.7 - - - +
65D ASP* 3.1 35.6 + - + +
97D TRP* 2.8 22.8 + - - -
98D PHE* 1.3 83.3 - - + +
100D TYR* 1.3 69.6 + - - +
109D TYR* 4.6 2.7 - - - -
112D ARG* 2.8 37.2 + - - +
113D VAL* 6.4 1.3 - - - +
116D MET* 4.1 3.1 - - - -
166D ARG* 2.7 30.1 + - - -
172D TYR* 3.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D PRO* 3.4 31.8 - - + +
62D GLU 3.4 22.6 + - - -
63D GLY 3.1 16.4 - - - -
64D SER* 4.1 0.2 - - - -
97D TRP* 3.8 13.0 - + - +
99D ASP* 1.3 84.4 + - - +
101D VAL* 1.3 64.3 + - - +
102D THR* 3.4 34.8 + - + +
112D ARG* 3.6 36.2 + - - +
115D ASP* 3.7 15.8 - - + +
116D MET* 3.7 30.3 - - + -
119D TYR* 3.9 18.8 - + + -
----------------------------------------------------------
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