Contacts of the helix formed by residues 62 - 75 (chain D) in PDB entry 1TU8
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 GLN 62 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C MET* 3.5 19.3 - - + +
92C GLU* 3.4 27.4 - - + +
93C GLY* 3.5 19.4 - - - -
96C ASP* 2.9 22.2 + - - +
47D PHE* 3.5 22.8 - - + +
49D GLN* 5.9 0.4 - - - +
51D PRO 3.8 6.3 + - - -
61D VAL* 1.3 81.0 - - - +
63D SER* 1.3 66.1 + - - +
64D GLY 3.2 1.7 + - - -
65D ALA* 3.0 10.3 + - + -
66D ILE* 2.9 22.9 + - - +
2003D GTX 2.9 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.0 23.8 - - - +
17D ILE* 3.9 14.5 - - - +
51D PRO* 4.0 15.8 - - - +
62D GLN* 1.3 70.5 - - - +
64D GLY* 1.3 59.5 + - - +
66D ILE* 3.5 6.0 + - - +
67D LEU* 3.1 25.2 + - - +
95D ARG* 2.8 22.0 + - - -
2003D GTX 2.5 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 4.5 3.4 + - - -
62D GLN 3.2 0.8 - - - -
63D SER* 1.3 80.9 + - - +
65D ALA* 1.3 56.6 + - - +
67D LEU* 3.4 5.5 + - - +
68D ARG* 3.0 57.6 + - - +
95D ARG* 3.3 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C THR* 4.3 5.5 - - - +
88C ASP* 3.5 22.9 - - + +
89C MET* 3.6 37.7 - - + +
92C GLU* 4.6 1.0 - - + +
60D ILE* 4.5 4.7 - - + -
61D VAL 4.0 5.6 - - - +
62D GLN* 3.0 12.3 + - + +
64D GLY* 1.3 72.3 - - - +
66D ILE* 1.3 65.0 + - - +
68D ARG* 3.6 3.5 - - - +
69D HIS* 3.0 26.0 + - - +
72D ARG* 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LEU* 4.8 0.9 - - + -
17D ILE* 3.8 32.5 - - + -
51D PRO* 3.9 21.3 - - + +
52D CYS 4.3 0.7 - - - -
53D LEU* 3.8 37.0 - - + +
60D ILE* 3.5 38.6 - - + +
61D VAL 4.1 0.4 - - - +
62D GLN 2.9 22.4 + - - +
63D SER* 3.7 11.0 - - - +
65D ALA* 1.3 76.4 - - - +
67D LEU* 1.3 58.7 + - - +
69D HIS* 3.2 4.9 + - - +
70D LEU* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 4.3 20.4 - - + +
17D ILE* 4.3 16.4 - - + -
20D PHE* 3.8 37.9 - - + -
63D SER 3.1 15.2 + - - +
64D GLY* 3.9 5.8 - - - +
66D ILE* 1.3 82.6 - - - +
68D ARG* 1.3 56.4 + - - +
70D LEU* 3.4 5.4 + - + +
71D ALA* 2.9 29.0 + - - +
91D CYS* 4.3 12.6 - - - -
149D TYR* 3.5 42.1 - - + +
152D TYR* 5.4 0.2 - - + -
153D ALA* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ARG* 3.6 41.1 - - - +
88C ASP* 2.8 40.1 + - - +
92C GLU* 3.5 22.6 - - - -
64D GLY* 3.0 40.2 + - - +
65D ALA 4.1 0.2 - - - +
67D LEU* 1.3 76.2 - - - +
69D HIS* 1.3 56.8 + - - +
71D ALA* 3.6 6.8 - - - +
72D ARG* 3.0 49.6 + - - +
77D ASN* 5.0 4.5 - - - +
88D ASP* 3.9 7.7 + - - -
91D CYS* 6.0 3.0 - - - +
92D GLU* 3.8 12.3 + - - -
95D ARG* 5.6 1.0 - - - +
149D TYR* 3.7 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 2.8 33.3 - - + +
85C THR* 3.1 26.0 - - + +
53D LEU* 4.3 9.9 - - + +
55D ASP* 2.7 32.0 + - + -
58D GLN* 4.1 8.7 + - - -
60D ILE* 3.7 23.5 - - + +
65D ALA 3.0 18.8 + - - +
66D ILE* 3.6 4.0 - - - +
68D ARG* 1.3 73.9 - - - +
70D LEU* 1.3 68.3 + - + +
72D ARG* 3.3 14.2 + - - +
73D LYS* 3.1 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TYR* 4.0 22.7 - - + +
17D ILE* 3.9 28.3 - - + -
20D PHE* 3.5 30.2 - - + -
21D LEU* 4.1 24.7 - - + -
26D ILE* 5.4 3.4 - - + -
53D LEU* 3.9 22.7 - - + -
66D ILE* 2.9 26.6 + - + +
67D LEU* 3.8 7.0 - - + +
69D HIS* 1.3 81.1 - - + +
71D ALA* 1.3 62.5 + - - +
73D LYS* 3.4 6.9 + - + +
74D TYR* 3.0 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.9 9.4 - - - -
67D LEU 2.9 17.4 + - - +
68D ARG* 3.6 6.5 - - - +
69D HIS 3.2 0.2 - - - -
70D LEU* 1.3 75.3 - - - +
72D ARG* 1.3 59.7 + - - +
74D TYR 3.4 0.2 + - - -
75D ASN* 2.9 11.6 + - - -
76D LEU* 2.9 34.8 + - - +
77D ASN* 3.7 7.8 + - + -
149D TYR* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 3.0 29.6 + - - +
84C THR* 3.7 23.4 + - - +
85C THR* 3.1 40.6 + - - +
88C ASP* 4.7 5.3 + - - -
65D ALA 4.9 1.2 + - - -
68D ARG* 3.0 36.4 + - - +
69D HIS* 3.3 15.7 + - - +
71D ALA* 1.3 76.9 - - - +
73D LYS* 1.3 63.3 + - - +
74D TYR 3.3 0.5 + - - -
75D ASN* 3.5 8.0 + - - +
77D ASN* 3.7 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 5.0 9.9 - - + -
3D TYR* 2.9 25.3 + - + +
55D ASP* 2.7 39.1 + - - +
69D HIS* 3.1 35.1 + - + +
70D LEU* 3.8 7.2 - - + +
71D ALA 3.3 0.2 - - - -
72D ARG* 1.3 77.9 - - - +
74D TYR* 1.3 73.2 + - + +
75D ASN* 3.9 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TYR* 3.9 23.6 + + - -
20D PHE* 4.2 13.0 - + + -
24D GLN* 4.6 16.2 - - - +
26D ILE* 3.5 47.9 - - + +
70D LEU* 3.0 19.4 + - + +
73D LYS* 1.3 91.0 - - + +
75D ASN* 1.3 71.1 + - - +
76D LEU* 3.3 16.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA 2.9 6.0 + - - -
72D ARG* 3.5 9.0 + - - +
73D LYS 3.6 1.0 + - - +
74D TYR* 1.3 80.9 - - - +
76D LEU* 1.3 62.3 + - - +
77D ASN* 3.4 5.5 + - - +
78D GLY 4.4 15.4 + - - +
79D GLU* 4.8 12.5 + - - +
147D ILE 5.0 1.7 - - - +
----------------------------------------------------------
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