Contacts of the strand formed by residues 91 - 99 (chain D) in PDB entry 6B0B
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 91 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LYS* 5.0 8.7 - - + -
71D ALA* 4.4 23.3 - - + -
82D TYR* 6.4 0.2 - - + -
83D LEU* 4.7 19.7 - - + -
86D SER* 3.6 17.9 - - - +
87D PHE* 4.3 13.9 - + - -
90D GLY* 1.3 76.3 - - - +
92D LYS* 1.3 80.0 + - - +
93D TRP* 3.5 28.7 - + + -
110D ASP* 3.6 2.1 - - - -
111D SER* 2.9 52.9 + - - +
120D TYR* 6.3 0.2 - + - -
181D TYR* 4.7 14.6 - + + -
182D LYS 3.3 15.3 - - - +
183D ALA* 3.6 9.9 - - + -
184D LYS* 4.0 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D PHE* 1.3 86.4 - - - +
93D TRP* 1.3 65.2 + - - +
109D GLN* 3.2 11.8 - - - +
110D ASP* 2.6 37.6 + - - +
181D TYR* 3.5 0.2 - - - -
182D LYS* 2.9 38.8 + - + +
184D LYS* 4.5 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLN* 3.1 58.1 + - + -
70D LYS* 5.7 7.8 - - + +
91D PHE* 3.5 20.6 - + - -
92D LYS* 1.3 77.4 - - - +
94D GLU* 1.3 62.2 + - - +
95D ARG* 3.5 24.0 - - + -
107D VAL* 3.6 22.9 - - + -
108D THR* 3.5 1.7 - - - -
109D GLN* 2.8 80.1 + - + +
122D VAL* 5.1 1.1 - - + -
179D THR* 3.7 14.8 - - + -
180D THR 3.0 13.7 - - - +
181D TYR* 3.5 24.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D TRP* 1.3 74.3 - - - +
95D ARG* 1.3 60.3 - - - +
96D VAL* 5.7 1.6 - - + -
107D VAL 3.3 7.6 - - - +
108D THR* 4.5 11.9 - - + -
178D LYS 3.9 1.0 - - - +
179D THR* 3.4 2.7 - - - -
180D THR* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PRO* 2.4 43.0 + - - +
64D GLN* 3.3 18.9 + - - +
70D LYS* 3.7 17.0 - - - +
93D TRP* 3.5 20.5 - - + -
94D GLU* 1.3 74.2 - - - +
96D VAL* 1.3 68.7 + - - +
97D MET* 3.8 14.4 - - + -
105D VAL 3.6 1.3 - - - +
106D THR* 3.4 4.3 - - - -
107D VAL* 2.9 34.8 + - + +
148D GLU* 5.3 1.8 + - - -
161D ILE* 5.5 5.3 - - - +
177D VAL* 3.6 24.5 - - + +
178D LYS 3.4 3.1 - - - -
179D THR* 2.5 26.6 + - + +
181D TYR* 2.8 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU* 5.7 1.6 - - + -
95D ARG* 1.3 78.6 - - - +
97D MET* 1.3 63.6 + - - +
98D ASN* 4.2 24.2 - - - +
104D VAL* 5.0 3.6 - - + -
105D VAL 3.4 5.8 - - - +
106D THR* 4.4 17.7 - - + -
176D GLU 3.7 2.1 - - - +
177D VAL* 3.5 1.9 - - - -
178D LYS* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ILE 4.5 5.6 - - - +
63D PRO* 4.8 5.4 - - + -
64D GLN* 3.3 30.7 - - - +
95D ARG* 3.8 11.2 - - + -
96D VAL* 1.3 76.6 - - - +
98D ASN* 1.3 63.4 + - - +
99D PHE* 3.9 28.5 - - + -
103D GLY 3.7 1.4 - - - +
104D VAL* 3.4 5.2 - - - +
105D VAL* 2.9 55.0 + - + +
107D VAL* 5.5 0.2 - - - -
143D TRP* 4.5 17.5 - - + -
163D GLN* 4.5 5.2 - - - +
175D ALA* 5.3 1.6 - - + -
176D GLU 3.5 4.5 - - - -
177D VAL* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D VAL* 4.1 14.5 - - - +
97D MET* 1.3 70.6 - - - +
99D PHE* 1.3 65.2 + - - +
103D GLY 3.6 1.8 - - - +
104D VAL* 3.4 32.2 - - - +
175D ALA* 3.4 1.4 - - - -
176D GLU* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ILE* 4.1 22.0 - - + -
97D MET* 3.9 30.1 - - + -
98D ASN* 1.3 76.9 - - - +
100D GLU* 1.3 65.0 + - - +
101D ASP* 3.2 7.0 + - - +
102D GLY* 3.2 13.0 + - - -
103D GLY* 2.7 22.5 + - - +
105D VAL* 3.7 14.4 - - + -
129D PHE* 3.5 27.8 - + - -
135D VAL* 4.7 1.1 - - + -
143D TRP* 3.9 23.8 - + - -
165D LEU* 5.0 0.7 - - + -
173D TYR* 3.1 42.6 - + - +
174D ASP 4.7 0.2 - - - -
175D ALA* 3.6 16.4 - - + -
----------------------------------------------------------
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