Contacts of the strand formed by residues 91 - 100 (chain C) 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 THR 91 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.2 13.2 - - + -
11C GLY 3.2 6.7 - - - -
12C VAL* 4.2 21.3 - - + -
77C LEU* 4.2 2.5 - - - -
89C SER* 5.8 1.1 - - - +
90C HIS* 1.3 78.8 - - - +
92C TYR* 1.3 59.2 + - - +
93C GLN* 4.2 1.9 + - - -
114C TYR* 3.6 10.0 - - - -
115C ASP* 2.9 37.9 + - - +
116C GLY 3.8 1.0 + - - -
31F HIS* 3.1 34.5 + - + -
32F PRO* 4.4 15.5 - - + -
33F SER* 5.7 2.0 - - - +
62F PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY 2.8 33.4 + - - +
73C PHE* 3.2 46.9 - + + -
76C GLU* 2.7 48.5 + - + +
77C LEU* 3.8 23.1 - - + +
80C LEU* 3.6 29.5 - - + +
91C THR* 1.3 76.0 - - - +
93C GLN* 1.3 65.1 + - - +
112C TYR* 3.3 32.4 - + + -
113C ALA 3.4 14.6 - - - -
114C TYR* 5.3 0.2 - - + -
119C PHE* 4.9 5.1 - + - -
143C TRP* 3.9 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C PHE* 5.5 3.7 - - + -
9C ARG 3.3 9.9 - - - +
10C LEU* 3.6 15.3 - - + -
73C PHE* 3.8 3.6 - - - -
91C THR* 4.2 2.6 + - - -
92C TYR* 1.3 80.3 - - - +
94C ARG* 1.3 59.0 + - - +
112C TYR* 3.2 10.0 - - - -
113C ALA* 2.7 39.0 + - + +
116C GLY* 3.9 6.8 + - - -
31F HIS* 3.0 23.7 + - - -
56F PHE* 4.4 8.4 - - + +
57F SER 5.5 0.2 + - - -
60F TRP* 3.1 56.4 + - + +
62F PHE* 3.5 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR 4.4 1.5 + - - +
8C PHE* 3.2 10.5 - - - +
9C ARG* 3.0 64.3 + - + +
73C PHE* 3.7 18.1 - - + -
93C GLN* 1.3 73.8 - - - +
95C MET* 1.3 64.7 + - - +
96C ILE* 3.8 20.6 - - - +
110C LEU* 3.8 15.9 - - + +
111C GLN 3.4 7.9 - - - +
112C TYR* 2.8 38.7 + - + -
153C GLN* 4.2 8.9 - - - +
301C 2LJ 3.0 55.9 + - - -
60F TRP* 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 4.1 13.0 - - + -
7C TYR 3.4 5.4 - - - +
8C PHE* 3.7 37.9 - - + -
94C ARG* 1.3 75.4 - - - +
96C ILE* 1.3 68.6 + - - +
109C PHE* 3.4 33.5 - - + +
110C LEU* 3.3 6.5 - - - +
111C GLN* 2.9 55.3 + - + +
58F LYS* 3.8 27.8 - - + +
60F TRP* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ARG* 3.2 6.1 - - - +
7C TYR* 3.0 56.0 + - + +
94C ARG* 3.8 14.6 - - - +
95C MET* 1.3 74.8 - - - +
97C GLY* 1.3 63.0 + - - +
109C PHE* 3.4 16.2 - - - +
110C LEU* 3.8 14.6 - - + -
153C GLN* 3.4 26.7 - - - +
156C TRP* 3.8 17.3 - - + -
157C LEU* 3.6 11.4 - - + -
301C 2LJ 3.5 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU 3.0 13.7 - - - -
7C TYR* 6.1 0.4 - - - -
96C ILE* 1.3 80.1 - - - +
98C CYS* 1.3 61.5 + - - -
108C GLY* 3.4 0.9 - - - -
109C PHE* 2.9 45.5 + - - -
156C TRP* 5.6 0.2 - - - -
157C LEU* 3.3 9.2 - - - +
161C CYS* 3.7 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C SER* 3.3 5.0 - - - -
5C LEU* 2.9 39.0 + - - +
97C GLY* 1.3 73.8 - - - +
99C GLU* 1.3 64.1 + - - +
107C THR 3.2 14.8 - - - +
109C PHE* 3.5 5.1 - - - -
157C LEU 3.8 5.6 - - - +
161C CYS* 2.1 63.7 - - + -
162C ILE* 3.7 16.6 - - + -
165C LEU* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 4.7 11.7 - - + +
3C HIS 3.3 8.3 - - - +
4C SER* 3.7 19.6 - - - -
98C CYS* 1.3 79.2 - - - +
100C LEU* 1.3 60.7 + - - +
101C LEU* 3.7 15.3 + - + +
106C THR* 3.2 11.4 - - - -
107C THR* 3.0 56.0 + - - +
109C PHE* 4.1 12.2 - - + -
162C ILE* 3.7 4.2 - - - +
58F LYS* 5.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C MET* 4.0 25.6 - - + -
1C ARG 4.0 3.1 - - - +
2C THR* 3.4 1.3 - - - -
3C HIS* 2.9 30.2 + - + +
99C GLU* 1.3 69.4 - - - +
101C LEU* 1.3 69.5 + - - +
104C GLY* 4.0 16.4 - - - +
105C SER 3.9 1.6 - - - +
106C THR* 3.9 21.5 - - + -
162C ILE* 4.5 7.6 - - + +
165C LEU* 3.8 17.3 - - + +
166C LYS* 3.9 41.3 - - + +
169C LEU* 4.6 6.1 - - + -
----------------------------------------------------------
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