Contacts of the helix formed by residues 58 - 69 (chain B) in PDB entry 1A7A
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 VAL 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.7 30.3 - - + +
22B LEU* 3.7 14.4 - - + -
25B ALA* 3.5 27.6 - - + -
57B THR* 1.3 70.4 - - - +
59B GLU* 1.3 75.2 + - - +
61B ALA* 3.0 18.0 + - - +
62B VAL* 3.2 6.8 + - - +
85B GLN* 2.7 26.3 - - - +
87B HIS* 3.8 13.9 - - + +
88B ALA* 3.5 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MSE 3.1 30.6 - - + +
57B THR* 3.2 11.6 + - - +
58B VAL* 1.3 85.1 + - - +
60B THR* 1.3 55.9 + - - +
62B VAL* 2.7 27.9 + - - +
63B LEU 3.1 7.6 + - - -
85B GLN* 4.3 1.6 + - - +
351B MSE 4.2 4.1 - - - +
353B HIS 4.0 6.6 - - - +
354B PRO* 5.3 0.2 - - - +
355B SER* 3.1 30.0 + - - +
358B MSE 3.9 11.7 - - + -
362B PHE* 3.7 20.3 - - + -
436B ADC 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.2 14.0 - - + +
55B HIS 2.5 28.7 + - - +
56B MSE 4.4 2.2 - - - -
57B THR* 2.9 18.7 + - - -
59B GLU* 1.3 78.3 - - - +
61B ALA* 1.3 52.1 + - - +
63B LEU* 3.0 5.5 + - + +
64B ILE* 2.7 43.4 + - + +
76B TRP* 3.5 41.1 - - + +
362B PHE* 3.5 11.4 - - + -
436B ADC 3.4 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.4 23.8 - - + -
56B MSE 4.7 1.5 - - + -
57B THR 2.9 10.5 + - - +
58B VAL* 3.0 13.6 + - - +
60B THR* 1.3 76.2 - - - +
62B VAL* 1.3 60.2 + - - +
64B ILE* 3.3 6.7 + - - +
65B GLU* 3.0 29.3 + - - +
88B ALA* 4.5 5.4 - - + +
92B ILE* 3.7 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.3 9.6 - - + +
25B ALA* 4.2 11.2 - - + -
26B GLU* 4.0 28.9 - - + +
29B MSE 3.8 22.9 - - + -
32B LEU* 3.7 16.2 - - + -
33B MSE 4.4 9.4 - - - -
36B ARG* 2.8 29.2 + - - +
58B VAL 3.7 12.6 - - - +
59B GLU 2.7 12.7 + - - +
61B ALA* 1.3 72.7 - - - +
63B LEU* 1.3 56.3 + - - +
65B GLU* 4.9 2.0 - - - -
66B THR* 2.6 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.8 8.0 - - + +
54B LEU* 4.6 1.8 - - + -
59B GLU 3.1 4.0 + - - -
60B THR 3.0 8.6 + - - +
62B VAL* 1.3 75.1 - - - +
64B ILE* 1.3 60.4 + - - +
66B THR* 2.7 25.0 + - - -
67B LEU* 2.9 24.2 + - + +
76B TRP* 4.2 13.7 - - + -
129B LEU* 4.2 19.7 - - + -
362B PHE* 3.4 57.4 - - + +
365B GLN* 4.3 5.8 - - + -
366B VAL* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MSE 3.6 39.5 - - + -
60B THR* 2.7 27.5 + - + +
61B ALA* 3.5 8.3 - - - +
63B LEU* 1.3 73.5 - - - +
65B GLU* 1.3 62.9 + - - +
67B LEU* 3.2 11.9 + - - +
68B VAL* 3.1 21.3 + - - +
74B VAL* 4.3 13.6 - - + +
76B TRP* 3.8 34.5 - - + -
92B ILE* 4.2 6.3 - - + -
97B ILE* 4.0 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 2.7 48.3 + - - +
22B LEU* 3.2 16.3 - - - +
26B GLU* 4.5 4.5 - - - +
36B ARG* 3.4 24.6 + - - +
61B ALA 3.0 12.5 + - - +
62B VAL* 5.5 0.4 - - - -
64B ILE* 1.3 73.6 - - - +
66B THR* 1.3 61.4 + - - +
68B VAL* 3.2 9.6 + - + +
69B THR* 2.8 32.8 + - - +
92B ILE* 3.8 14.7 - - + +
95B ALA* 5.5 1.6 - - + -
97B ILE* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.8 21.6 - - + +
35B MSE 4.5 6.5 - - + -
36B ARG* 2.8 37.8 + - + +
62B VAL 2.6 20.9 + - - -
63B LEU* 2.7 18.3 + - - -
65B GLU* 1.3 69.4 - - - +
67B LEU* 1.3 66.5 + - - +
69B THR* 3.1 1.6 + - - -
70B LEU* 3.0 37.2 + - + +
366B VAL* 4.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.8 21.8 - - + -
50B ILE* 3.9 22.9 - - + -
63B LEU* 2.9 23.2 + - + +
64B ILE* 3.5 8.3 - - - +
66B THR* 1.3 75.7 - - - +
68B VAL* 1.3 63.0 + - - +
70B LEU* 3.1 14.0 + - - +
71B GLY 3.2 7.4 + - - -
72B ALA* 3.3 12.6 + - - +
74B VAL* 4.1 14.1 - - + -
76B TRP* 4.1 17.3 - - + -
129B LEU* 3.9 23.8 - - + -
366B VAL* 4.3 22.9 - - + -
369B GLN* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 4.5 2.8 + - - -
64B ILE 3.1 13.6 + - - +
65B GLU* 3.4 10.3 - - + +
66B THR 3.1 0.4 - - - -
67B LEU* 1.3 73.2 - - - +
69B THR* 1.3 58.4 + - - +
70B LEU 2.9 2.0 - - - -
71B GLY* 2.5 27.2 + - - -
72B ALA 3.9 17.7 + - - +
74B VAL* 4.2 10.8 - - + +
97B ILE* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 4.3 22.5 + - + +
40B SER* 3.3 36.4 - - - +
43B LYS* 2.9 30.2 + - - +
65B GLU* 2.8 23.6 + - - +
66B THR* 3.1 8.7 + - - -
68B VAL* 1.3 75.3 - - - +
70B LEU* 1.3 61.9 + - + +
71B GLY 3.1 0.2 - - - -
----------------------------------------------------------
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