Contacts of the helix formed by residues 60 - 71 (chain D) in PDB entry 3LBF
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 60 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 5.5 1.5 + - - +
47D ASN* 3.1 38.6 + - - +
48D ILE* 3.3 10.6 - - - +
49D ALA* 3.3 29.7 - - + +
59D SER* 1.3 74.5 - - - +
61D PRO* 1.3 71.0 - - + +
62D TYR* 3.6 27.1 - - - +
63D MET* 2.9 31.4 + - + +
64D VAL 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 5.6 5.2 - - + -
13D LEU* 4.3 18.3 - - + +
32D ARG* 3.4 35.0 - - - +
45D TRP 4.7 5.2 - - - +
46D ASP 3.6 16.8 - - - +
47D ASN* 3.2 19.5 - - + +
48D ILE 3.9 0.9 - - - +
59D SER 3.5 1.8 - - - +
60D GLN* 1.3 84.3 - - + -
62D TYR* 1.3 55.6 + - - +
64D VAL* 3.4 7.5 + - + +
65D ALA* 2.8 31.2 + - - +
88D TYR* 4.9 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 3.5 11.6 - - + +
16D GLN* 3.6 52.0 + - + +
17D GLY 5.5 0.7 - - - -
18D ILE* 3.8 24.7 - - + -
47D ASN* 3.0 25.1 - - - +
60D GLN* 3.1 20.8 + - - +
61D PRO* 1.3 74.8 - - - +
63D MET* 1.3 65.3 + - + +
65D ALA* 3.3 2.2 + - - +
66D ARG* 2.8 55.6 + - + +
195D GLU* 3.8 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D SER* 4.4 8.1 - - - -
60D GLN* 2.9 25.4 + - + +
62D TYR* 1.3 88.3 - - + +
64D VAL* 1.3 60.9 + - - +
66D ARG* 3.3 3.8 + - - -
67D MET* 2.8 53.1 + - - +
179D LEU* 4.1 14.1 - - - -
195D GLU* 3.7 32.5 - - - +
197D VAL* 4.1 11.9 - - + -
199D PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D SER* 3.6 39.5 - - - +
60D GLN 3.1 2.4 + - - +
61D PRO* 3.7 9.2 - - + +
63D MET* 1.3 75.9 - - - +
65D ALA* 1.3 60.1 + - - +
67D MET* 4.0 2.6 - - - -
68D THR* 2.6 33.9 + - - +
88D TYR* 4.2 21.3 - - + +
89D GLN* 3.3 37.6 - - + +
92D ILE* 4.3 19.5 - - + -
300D SAH 5.6 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
13D LEU* 4.3 9.0 - - + -
18D ILE* 3.6 29.6 - - + -
23D VAL* 3.8 18.2 - - + +
24D LEU* 5.5 2.0 - - + -
61D PRO 2.8 21.9 + - - +
62D TYR* 3.5 6.1 - - - +
64D VAL* 1.3 75.7 - - - +
66D ARG* 1.3 52.8 + - - +
68D THR* 3.7 1.7 - - - -
69D GLU* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 5.8 2.9 - - - -
18D ILE* 3.5 12.0 - - + +
62D TYR* 2.8 49.9 + - + +
63D MET* 3.7 7.0 - - - +
65D ALA* 1.3 71.5 - - - +
67D MET* 1.3 66.1 + - - +
69D GLU* 2.9 31.4 + - - +
70D LEU* 3.0 69.2 + - + +
179D LEU* 4.9 6.5 - - + -
194D VAL* 5.1 11.2 - - + +
195D GLU* 4.7 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D SER* 5.6 1.6 - - - -
63D MET* 2.8 39.5 + - - +
64D VAL* 4.1 4.5 - - - +
66D ARG* 1.3 72.1 - - - +
68D THR* 1.3 62.4 - - - +
70D LEU* 3.3 18.5 + - - +
71D LEU* 3.4 18.0 + - - +
89D GLN* 4.7 2.2 - - - +
146D ILE* 3.8 28.7 - - + +
147D VAL 3.3 26.9 - - - +
148D THR* 4.8 4.3 - - + -
169D VAL* 4.0 17.2 - - + +
171D PRO* 4.3 3.6 - - + -
179D LEU* 4.0 20.9 - - + -
199D PHE* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 4.0 15.2 - - + +
64D VAL* 2.6 24.3 + - - +
65D ALA 3.7 2.7 - - - -
67D MET* 1.3 76.8 - - - +
69D GLU* 1.3 63.8 - - - +
71D LEU* 3.2 24.1 + - - +
72D GLU 3.9 2.3 + - - -
73D LEU* 4.1 8.0 + - + +
89D GLN* 2.9 24.5 + - - +
92D ILE* 4.4 3.8 - - + +
93D LEU* 3.9 17.0 - - + -
96D LEU* 3.5 31.6 - - + -
146D ILE* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 4.2 3.9 - - - +
18D ILE* 3.9 12.7 - - + +
19D GLN* 2.7 35.9 + - - +
20D ASP* 3.0 28.9 + - + +
23D VAL* 4.1 10.0 - - + +
65D ALA 2.8 17.9 + - - +
66D ARG* 2.9 36.2 + - - +
67D MET 3.2 0.2 - - - -
68D THR* 1.3 77.7 - - - +
70D LEU* 1.3 61.7 + - - +
72D GLU* 3.1 19.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
66D ARG* 3.0 52.2 + - + +
67D MET* 3.6 8.5 - - - +
68D THR 3.3 0.6 - - - -
69D GLU* 1.3 74.8 - - - +
71D LEU* 1.3 60.5 + - - +
72D GLU* 3.2 10.2 + - - +
167D ILE* 3.7 16.3 - - - +
169D VAL* 3.7 20.4 - - + -
179D LEU* 4.0 26.9 - - + -
181D ARG* 4.0 27.5 + - - +
194D VAL* 4.2 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
67D MET 3.5 9.9 - - - +
68D THR* 3.4 9.4 - - - +
69D GLU 3.1 1.0 - - - -
70D LEU* 1.3 75.1 - - - +
72D GLU* 1.3 70.2 + - - +
73D LEU* 3.3 35.9 + - + +
79D VAL* 4.9 2.7 - - + -
93D LEU* 4.1 8.3 - - + -
143D ASP 5.1 1.2 - - - +
144D ALA* 4.2 13.3 - - + +
145D ILE 3.5 28.0 - - - +
146D ILE* 3.8 31.9 - - + -
167D ILE* 4.0 23.1 - - - +
169D VAL* 3.7 20.9 - - + -
----------------------------------------------------------
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