Contacts of the helix formed by residues 70 - 88 (chain S) in PDB entry 1EQY
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 SER 70 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLY 4.3 0.2 + - - -
68S GLU 3.8 2.2 + - - -
69S CYS* 1.3 76.2 - - - +
71S GLN* 1.3 61.0 + - - +
72S ASP* 2.8 21.8 + - - -
73S GLU* 3.0 41.1 + - - +
74S SER* 3.2 11.6 + - - -
123S SER* 3.6 19.2 + - - -
125S PHE* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA* 3.1 39.5 + - - +
334A GLU* 3.0 31.4 + - - +
338A SER* 5.5 1.2 + - - +
341A ILE* 3.9 31.1 - - + +
345A ILE* 3.9 4.2 - - + +
69S CYS 4.0 0.2 + - - -
70S SER* 1.3 73.5 - - - +
72S ASP* 1.3 58.3 + - - +
74S SER* 3.2 8.9 + - - +
75S GLY* 3.0 25.5 + - - -
125S PHE* 4.2 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.1 10.4 - - - +
22S VAL* 5.0 0.4 - - - +
24S LYS* 5.1 4.0 - - - -
25S PHE* 3.8 23.9 + - + -
70S SER* 2.8 24.7 + - - -
71S GLN* 1.3 75.8 + - - +
73S GLU* 1.3 68.1 + - - +
75S GLY 4.1 0.3 - - - -
76S ALA* 3.1 29.6 + - - +
123S SER* 3.0 15.3 + - - -
124S GLY* 3.1 23.9 + - - -
125S PHE* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S VAL* 4.1 23.5 - - + +
24S LYS 5.4 3.5 + - - +
41S GLY 3.1 9.4 - - - +
42S ASP* 3.2 11.0 - - - +
43S ALA* 3.7 17.0 - - + +
69S CYS* 3.6 3.0 - - + +
70S SER* 3.0 32.7 + - - +
72S ASP* 1.3 86.0 - - - +
74S SER* 1.3 64.9 + - - +
76S ALA* 3.3 1.6 + - - +
77S ALA* 3.1 25.3 + - - +
121S VAL* 3.3 17.9 - - - +
122S ALA 4.2 4.3 - - - +
123S SER* 5.0 2.0 - - - -
395S CA 2.6 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 5.0 0.9 + - - -
145A SER 5.3 0.9 - - - -
146A GLY* 3.6 19.9 + - - +
43S ALA* 4.3 1.5 - - - +
63S TYR* 4.9 0.3 - - - -
65S LEU* 3.9 32.3 - - - +
69S CYS* 3.9 18.6 - - - -
70S SER 3.2 7.1 + - - -
71S GLN* 3.2 17.2 + - - +
73S GLU* 1.3 79.1 - - - +
75S GLY* 1.3 62.2 + - - +
77S ALA* 3.7 2.6 + - - +
78S ALA* 3.4 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR 3.4 23.5 - - - +
144A ALA 5.1 0.4 - - - -
146A GLY* 4.3 1.5 - - - +
345A ILE* 4.2 14.8 - - - -
71S GLN 3.0 16.9 + - - -
72S ASP 4.2 0.7 - - - -
74S SER* 1.3 78.8 + - - +
76S ALA* 1.3 59.8 + - - +
78S ALA* 3.5 3.6 + - - +
79S ILE* 3.2 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.1 4.0 - - + +
349A LEU* 3.5 30.4 - - + +
22S VAL* 4.0 17.5 - - + -
25S PHE* 4.9 4.7 - - + -
72S ASP 3.1 21.5 + - - +
73S GLU 3.3 2.6 + - - +
75S GLY* 1.3 73.0 - - - +
77S ALA* 1.3 67.1 + - - +
79S ILE* 3.3 3.1 + - - +
80S PHE* 2.9 34.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S VAL* 3.9 18.9 - - + +
43S ALA* 4.3 10.1 - - + -
44S TYR 4.2 6.1 - - - +
45S VAL* 3.7 14.2 - - + +
63S TYR* 4.0 18.6 - - + -
65S LEU* 4.5 3.6 - - + -
73S GLU 3.1 15.9 + - - +
74S SER 4.0 5.2 - - - +
76S ALA* 1.3 76.6 - - - +
78S ALA* 1.3 60.9 + - - +
80S PHE* 4.5 0.2 - - - -
81S THR* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 5.0 3.8 - - + +
146A GLY* 4.0 1.1 - - - -
147A ARG 4.0 17.5 - - - +
148A THR* 3.1 38.0 - - + +
63S TYR* 3.7 21.0 - - + -
74S SER 3.4 9.2 + - - +
75S GLY 3.7 8.7 - - - +
76S ALA 3.2 0.6 - - - -
77S ALA* 1.3 77.6 - - - +
79S ILE* 1.3 66.6 + - + +
81S THR* 3.3 2.3 + - - -
82S VAL* 3.2 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.9 41.7 - - + -
342A GLY 4.9 0.2 - - - +
345A ILE* 4.1 11.9 - - + -
346A LEU* 3.9 37.5 - - + +
349A LEU* 3.3 27.1 - - + -
75S GLY 3.2 17.8 + - - +
76S ALA 3.3 1.1 + - - +
78S ALA* 1.3 72.1 - - - +
80S PHE* 1.3 65.6 + - - +
81S THR 3.0 2.2 + - - -
82S VAL* 3.1 11.0 + - + +
83S GLN* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.1 15.0 - - + -
350A SER* 4.6 1.6 - - - -
351A THR* 3.3 34.8 - - + -
8S PHE* 4.7 2.0 - + - -
22S VAL* 4.2 9.9 - - + -
25S PHE 4.0 12.6 - - - -
26S ASP* 3.8 25.4 - - - -
27S LEU* 3.7 39.3 - - + -
45S VAL* 4.3 8.7 - - + -
76S ALA* 2.9 36.0 + - + +
77S ALA 3.8 4.7 - - - +
79S ILE* 1.3 75.9 - - - +
81S THR* 1.3 57.3 + - - +
83S GLN* 3.3 17.9 + - - +
84S LEU* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S VAL* 4.0 12.2 - - - +
61S LEU* 3.5 25.6 - - + +
62S HIS 4.9 0.3 - - - -
63S TYR* 3.6 31.6 + - + +
77S ALA 2.9 15.8 + - - -
78S ALA 3.3 11.7 - - - +
79S ILE 3.0 0.4 - - - -
80S PHE* 1.3 75.4 - - - +
82S VAL* 1.3 66.3 + - - +
84S LEU* 3.2 4.3 + - - -
85S ASP* 3.0 20.3 + - - +
94S GLN* 3.5 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 4.4 14.1 - - + +
148A THR* 3.7 23.3 - - + -
167A GLU 4.1 11.2 - - - +
168A GLY* 3.8 16.8 - - - -
169A TYR* 4.0 13.7 - - + +
78S ALA 3.2 13.9 + - - +
79S ILE* 3.1 11.6 + - + +
81S THR* 1.3 76.8 - - - +
83S GLN* 1.3 65.0 + - + +
85S ASP* 3.2 3.8 + - - +
86S ASP* 3.1 36.8 + - - +
94S GLN* 3.8 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.8 1.6 - - - +
349A LEU* 4.3 4.2 - - - +
351A THR* 2.5 43.6 + - - +
352A PHE* 4.6 13.3 - - - -
355A MET* 4.9 8.9 - - + +
3S VAL* 5.1 7.6 - - + +
8S PHE* 3.9 12.9 - - + -
79S ILE* 2.9 34.6 + - + +
80S PHE* 3.4 20.9 - - - +
82S VAL* 1.3 78.0 - - + +
84S LEU* 1.3 63.4 + - - +
86S ASP* 3.5 8.9 + - - +
87S TYR* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S GLU 5.8 0.2 - - - -
8S PHE* 3.5 36.3 - - + -
11S ALA* 4.4 23.1 - - + -
20S TRP* 5.1 7.6 - - + -
27S LEU* 3.9 26.2 - - + -
45S VAL* 4.6 15.3 - - + -
47S LEU* 5.7 0.7 - - + -
61S LEU* 3.6 24.7 - - + -
80S PHE 2.8 30.2 + - - +
83S GLN* 1.3 73.4 - - - +
85S ASP* 1.3 59.6 + - - +
87S TYR* 3.6 6.4 + - + +
88S LEU* 3.0 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.4 1.9 - - - +
61S LEU* 3.7 7.8 - - + +
81S THR 3.0 7.5 + - - +
82S VAL 3.4 8.7 - - - +
84S LEU* 1.3 75.3 - - - +
86S ASP* 1.3 58.4 + - - +
88S LEU* 2.8 16.5 + - - +
90S GLY* 2.7 36.8 + - - -
92S ALA* 2.8 34.5 + - - +
94S GLN* 2.5 32.7 + - - +
390S CA 2.5 30.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU 5.3 0.2 - - - +
169A TYR* 2.4 43.3 + - - -
1S MET* 4.4 30.8 - - + +
82S VAL* 3.1 21.7 + - - +
83S GLN* 3.8 7.6 - - - +
85S ASP* 1.3 81.1 - - - +
87S TYR* 1.3 56.9 + - - +
89S ASN* 2.9 22.7 + - - -
90S GLY* 3.9 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 6.2 1.6 - - - -
2S VAL* 4.5 17.3 - - + -
3S VAL* 4.0 25.1 - - + -
8S PHE* 3.3 49.9 + + + -
9S LEU* 3.6 30.3 - - + +
11S ALA* 5.4 2.2 - - + -
83S GLN 3.0 17.7 + - - +
84S LEU* 3.7 7.4 - - + +
86S ASP* 1.3 76.9 - - - +
88S LEU* 1.3 72.4 + - + +
89S ASN* 3.1 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ALA* 4.4 17.7 - - + +
47S LEU* 4.6 14.8 - - + -
59S TYR* 4.1 49.3 - - + +
61S LEU* 4.8 2.7 - - + -
84S LEU* 3.0 26.9 + - + +
85S ASP* 2.8 9.4 + - - +
87S TYR* 1.3 89.0 - - + +
89S ASN* 1.3 73.5 + - - +
90S GLY 3.1 0.9 - - - -
91S ARG* 3.1 24.0 + - - +
92S ALA* 4.4 12.1 - - + +
----------------------------------------------------------
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