Contacts of the helix formed by residues 66 - 78 (chain D) in PDB entry 1EFP
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 LYS 66 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D VAL* 1.3 73.0 - - - +
67D GLN* 1.3 70.9 + - - +
68D ALA 2.9 6.6 + - - -
69D ALA* 3.1 18.9 + - - +
85D LEU* 3.6 11.1 - - + +
87D VAL* 4.0 24.6 - - + +
89D ALA 5.0 0.2 + - - -
205D GLU* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 3.7 35.5 + - - +
65D VAL* 3.1 23.4 + - - +
66D LYS* 1.3 76.1 + - - +
68D ALA* 1.3 57.5 + - - +
69D ALA* 2.8 13.2 + - - -
70D GLU* 3.0 23.5 + - - +
92D VAL* 5.0 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 3.8 21.8 - - + +
62D SER* 3.9 15.8 + - - +
63D ILE 5.1 0.9 - - - +
64D GLY* 5.1 4.3 - - - -
65D VAL* 2.9 24.1 + - + +
66D LYS 2.9 0.6 + - - -
67D GLN* 1.3 76.6 - - - +
69D ALA* 1.3 61.8 + - - +
70D GLU 3.2 0.2 - - - -
71D THR* 3.0 16.4 + - - -
72D LEU* 3.2 12.6 + - - +
85D LEU* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS 3.1 14.9 + - - +
67D GLN* 2.8 1.7 + - - +
68D ALA* 1.3 76.9 - - - +
70D GLU* 1.3 63.0 + - - +
72D LEU* 3.0 10.9 + - - +
73D ARG* 2.8 29.8 + - + +
85D LEU* 4.2 15.2 - - + +
203D LEU* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ARG* 4.8 13.1 + - - +
67D GLN* 3.0 14.8 + - - +
69D ALA* 1.3 77.4 - - - +
71D THR* 1.3 62.7 + - - +
73D ARG* 3.4 8.9 + - - +
74D THR* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.1 11.0 - - + -
8D LYS 4.0 14.1 - - - +
9D ARG* 3.3 33.0 - - - +
34D SER 4.6 4.9 + - - -
35D MET* 3.6 41.4 + - + +
62D SER* 5.1 2.5 - - - +
68D ALA 3.0 10.3 + - - -
70D GLU* 1.3 77.0 - - - +
72D LEU* 1.3 63.4 + - - +
74D THR* 3.3 10.9 - - - -
75D ALA 3.2 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.0 5.4 - - + -
60D ALA* 3.3 38.8 - - + +
61D VAL 3.9 10.3 - - - -
62D SER* 3.8 17.7 - - - -
68D ALA 3.2 4.2 + - - +
69D ALA* 3.0 9.9 + - - +
71D THR* 1.3 74.9 - - - +
73D ARG* 1.3 65.1 + - - +
75D ALA* 2.8 16.3 + - - +
76D LEU* 2.8 17.2 + - - +
83D ALA* 3.7 15.7 - - + -
84D ILE 3.5 21.3 - - - +
85D LEU* 3.7 25.6 - - + -
203D LEU* 3.9 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ALA* 2.8 22.5 + - + +
70D GLU* 3.7 9.4 - - - +
72D LEU* 1.3 74.9 - - - +
74D THR* 1.3 53.2 + - - +
76D LEU* 3.0 23.6 + - - +
77D ALA* 2.7 35.7 + - - +
198D ALA* 2.8 34.0 + - + +
199D LYS* 3.9 34.2 + - + +
201D LYS 2.5 32.5 + - - +
203D LEU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D MET* 4.8 15.9 - - + -
40D GLU* 5.6 3.8 - - - +
70D GLU* 3.0 19.8 + - - +
71D THR* 3.3 14.2 - - - -
72D LEU 3.1 0.6 - - - -
73D ARG* 1.3 76.5 - - - +
75D ALA* 1.3 61.0 + - - +
77D ALA* 3.3 9.8 + - + +
78D MET* 3.0 31.2 + - + +
190D ALA* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.9 2.5 - - + -
35D MET* 3.9 17.9 - - + +
43D VAL* 4.4 11.1 - - + +
60D ALA* 4.0 24.7 - - + -
71D THR 3.2 8.7 + - - +
72D LEU* 2.8 12.0 + - - +
74D THR* 1.3 75.3 - - - +
76D LEU* 1.3 66.6 + - - +
78D MET* 3.0 20.4 + - - +
79D GLY 3.1 9.4 + - - -
80D ALA* 3.1 11.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ALA* 5.4 0.2 - - + -
72D LEU 2.8 14.8 + - - +
73D ARG* 3.2 50.9 - - - +
75D ALA* 1.3 75.1 - - - +
77D ALA* 1.3 63.4 + - - +
79D GLY 3.1 7.6 + - - -
80D ALA* 3.2 24.1 + - + +
81D ASP 3.9 1.6 - - - -
82D ARG* 3.5 34.8 - - - +
83D ALA* 4.1 13.5 - - + -
198D ALA* 3.8 5.8 - - + +
201D LYS* 2.9 42.4 + - + -
202D PRO 4.4 2.7 - - - +
203D LEU* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ARG 2.7 16.8 + - - +
74D THR* 3.4 14.8 - - - +
76D LEU* 1.3 75.5 - - - +
78D MET* 1.3 60.6 + - - +
79D GLY* 4.5 0.2 - - - -
190D ALA* 3.6 22.7 - - + +
194D ASN* 3.4 28.7 + - - +
195D ILE* 4.2 16.2 - - + -
198D ALA* 3.8 17.0 - - + +
201D LYS* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D MET* 5.0 6.5 - - - +
40D GLU* 3.8 33.4 - - + +
43D VAL* 4.0 22.0 - - + -
44D GLU* 4.2 9.2 - - + +
47D ILE* 3.3 17.3 - - + +
74D THR* 3.0 25.4 + - + +
75D ALA* 3.0 12.4 + - - +
77D ALA* 1.3 78.9 - - - +
79D GLY* 1.3 57.1 + - - +
187D PRO* 4.2 12.3 - - + -
188D ARG* 3.4 49.8 + - + +
190D ALA* 4.3 14.6 - - + +
194D ASN* 4.9 5.6 + - - -
----------------------------------------------------------
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