Contacts of the strand formed by residues 65 - 79 (chain D) in PDB entry 1QD6
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 ASP 65 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 2.5 35.1 + - + +
43D THR 3.2 11.9 - - - +
44D GLN* 4.2 11.0 - - + +
63D ARG* 3.6 24.1 + - - +
64D LYS* 1.3 78.0 + - - +
66D GLU* 1.3 67.1 + - - +
99D GLN* 4.5 7.4 - - - -
100D LEU 4.8 1.4 + - - -
101D SER* 2.8 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 4.5 5.3 - - - -
43D THR* 2.8 40.8 + - - +
48D LEU* 4.0 2.8 - - - +
63D ARG 4.4 2.2 - - - +
64D LYS 4.0 0.2 + - - -
65D ASP* 1.3 80.8 - - - +
67D VAL* 1.3 66.8 + - - +
97D TRP* 3.7 11.3 - - + +
98D TRP 3.4 12.3 - - - +
99D GLN* 2.9 29.4 + - - +
100D LEU 5.0 0.9 - - - +
110D ARG* 2.8 50.0 + - - +
258D ARG* 2.5 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 3.3 32.5 - - + -
41D ILE 3.5 7.4 - - - +
42D TYR* 3.6 17.9 - - + -
66D GLU* 1.3 71.8 - - - +
68D LYS* 1.3 64.2 + - - +
69D PHE* 4.4 4.6 - - + -
96D SER 3.5 1.6 - - - +
97D TRP* 3.4 4.2 - - - -
98D TRP* 2.9 56.7 + - + +
100D LEU* 3.4 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 3.5 25.4 + - + +
40D LEU* 3.6 0.9 - - - +
41D ILE* 2.8 40.0 + - + +
43D THR* 3.8 20.4 - - + +
66D GLU 3.7 1.2 + - - -
67D VAL* 1.3 75.7 - - - +
69D PHE* 1.3 65.1 + - - +
95D LYS* 5.3 8.0 - - + +
96D SER 3.3 7.4 - - - +
97D TRP* 3.4 37.2 - - + +
224D GLU* 4.1 8.7 + - - -
240D GLN* 2.9 29.6 - - - +
242D TYR* 4.7 2.8 - - - +
247D GLU* 2.8 30.6 + - - +
258D ARG* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.9 12.8 - - - -
114C TYR* 4.7 0.4 - + - -
270C HDS 3.5 44.0 - - + -
39D TYR* 3.2 18.4 - - - +
40D LEU* 3.6 17.7 - - + -
67D VAL* 4.4 7.4 - - + -
68D LYS* 1.3 79.7 - - - +
70D GLN* 1.3 61.3 + - - +
71D LEU* 3.9 29.8 - - + -
94D GLN* 3.7 7.8 - - - +
95D LYS* 3.4 3.9 - - - +
96D SER* 2.9 58.8 + - - -
98D TRP* 5.1 4.7 - + + -
109D PHE* 3.9 22.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C HDS 4.3 4.0 - - - +
36D ASP* 3.6 11.4 - - - +
37D THR* 2.6 48.3 + - - +
38D ASN* 3.4 4.5 - - - +
39D TYR* 3.0 56.0 + - + +
69D PHE* 1.3 74.6 - - - +
71D LEU* 1.3 66.1 + - - +
72D SER* 4.7 0.2 - - - -
93D THR* 3.9 15.7 - - + -
94D GLN 3.1 11.7 - - - +
95D LYS* 2.7 37.8 + - + +
211D LYS* 4.4 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.6 14.1 - - + -
73C LEU* 5.3 12.1 - - + -
92C TYR* 3.6 31.2 - - + -
94C GLN* 3.9 8.7 - - - +
270C HDS 3.8 22.9 - - + -
38D ASN* 3.3 7.2 - - - +
69D PHE* 3.9 11.0 - - + -
70D GLN* 1.3 77.0 - - - +
72D SER* 1.3 64.0 + - - +
73D LEU* 5.5 3.8 - - + -
92D TYR* 3.8 3.5 - - + +
93D THR* 3.4 0.7 - - - -
94D GLN* 2.9 72.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PRO* 3.5 3.3 - - - +
35D TYR* 3.2 14.0 + - - +
36D ASP* 2.8 38.8 + - - +
37D THR 3.7 10.3 - - - -
38D ASN* 2.7 28.6 + - - +
71D LEU* 1.3 77.1 - - - +
73D LEU* 1.3 64.2 + - - +
92D TYR 3.3 4.5 - - - -
93D THR* 2.8 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.3 34.8 - - + -
38C ASN* 4.7 9.4 - - - +
71C LEU* 5.0 15.5 - - + -
73C LEU* 4.3 28.3 - - + -
265C LEU* 5.4 0.4 - - + -
32D LEU* 4.7 14.8 - - + -
33D TYR 3.3 10.8 - - - +
35D TYR* 3.6 5.7 - - - +
38D ASN* 4.9 0.2 - - - +
71D LEU* 5.5 3.6 - - + -
72D SER* 1.3 79.6 + - - +
74D ALA* 1.3 60.4 + - - +
75D PHE* 3.7 30.1 - - + -
91D SER* 3.2 6.9 - - - -
92D TYR* 3.0 34.0 + - + +
270D HDS 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.6 0.2 - - + -
22B MET* 3.7 34.8 - - + -
32D LEU* 6.0 0.5 - - - +
33D TYR* 2.8 28.0 + - + +
34D PRO 3.6 18.6 - - - +
35D TYR* 3.7 11.8 - - + +
73D LEU* 1.3 74.5 - - - +
75D PHE* 1.3 68.0 + - - +
76D PRO* 3.8 3.9 - - - +
90D ALA 3.5 5.6 - - - +
91D SER* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 4.7 1.1 - - - -
71C LEU* 5.5 0.2 - - + -
235C VAL* 6.2 0.2 - - + -
265C LEU* 3.6 40.4 - - + -
32D LEU* 5.5 0.9 - - + -
73D LEU* 3.7 36.6 - - + -
74D ALA* 1.3 79.2 - - - +
76D PRO* 1.3 68.8 - - - +
77D LEU* 3.2 7.6 + - + +
89D GLY* 4.5 0.7 - - - -
90D ALA* 2.6 55.0 + - + +
91D SER 4.0 7.2 - - - -
92D TYR* 3.9 24.2 - + + -
270D HDS 3.9 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 3.7 42.2 - - + +
232C THR* 5.0 1.0 - - - +
234C HIS* 4.5 13.5 + - + +
235C VAL* 3.7 15.9 - - - +
33D TYR* 3.8 27.1 - - + -
74D ALA 3.8 7.0 - - - +
75D PHE* 1.3 81.1 - - - +
77D LEU* 1.3 61.4 + - - +
78D TRP 3.8 0.7 - - - -
79D ARG* 4.1 15.5 - - + +
87D VAL* 4.3 13.0 - - + -
88D LEU 4.2 4.9 - - - +
89D GLY* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C THR* 3.9 21.3 + - - +
235C VAL* 4.2 22.3 - - + +
75D PHE* 3.2 15.5 + - + +
76D PRO* 1.3 74.6 - - - +
78D TRP* 1.3 64.4 + - + +
79D ARG* 4.2 1.3 + - - -
88D LEU* 3.0 23.0 + - + +
89D GLY* 4.1 8.5 - - - -
90D ALA* 4.0 19.3 - - + +
118D LEU* 4.1 15.9 - - + -
270D HDS 4.2 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 1.3 78.9 - - + +
79D ARG* 1.3 76.7 + - - +
80D GLY 3.7 1.0 + - - -
81D ILE* 3.7 48.7 + - + +
87D VAL* 3.5 1.3 - - - -
88D LEU* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET 2.8 23.1 + - - +
23B LEU* 3.7 22.0 + - + +
24B GLN 2.8 12.2 + - - -
25B GLU* 3.6 8.5 - - - +
233C LYS* 3.2 37.0 - - - +
234C HIS* 3.2 21.0 + - - -
33D TYR* 2.7 31.7 + - - -
76D PRO* 4.1 11.6 - - + +
77D LEU 4.2 0.6 + - - -
78D TRP* 1.3 84.1 + - - +
80D GLY* 1.3 62.7 + - - +
86D SER 3.9 6.1 - - - +
87D VAL* 4.2 15.3 - - + -
----------------------------------------------------------
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