Contacts of the helix formed by residues 79 - 97 (chain B) in PDB entry 3EGC
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 ASN 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASP* 3.1 23.5 + - - +
77B ILE 3.3 4.7 - - - +
78B GLU* 1.3 77.4 - - - +
80B VAL* 1.3 64.7 + - - +
81B PHE* 3.0 15.7 + - - +
82B PHE* 3.2 29.9 + - + -
83B ALA 3.2 8.5 + - - -
253B SER* 5.6 2.8 + - - -
254B HIS* 2.8 32.1 + - - -
255B ARG* 3.6 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.6 22.0 - - - +
80A VAL* 3.3 31.8 - - + +
255A ARG* 5.6 3.1 - - - +
78B GLU 3.5 2.8 + - - -
79B ASN* 1.3 73.2 + - - +
81B PHE* 1.3 67.1 + - - +
82B PHE 3.3 0.2 - - - -
83B ALA* 3.7 7.4 - - + -
84B GLU* 3.1 43.5 + - - +
254B HIS* 4.3 10.4 + - + +
255B ARG* 4.6 0.8 - - - +
283B LEU* 4.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 3.0 17.4 + - - +
80B VAL* 1.3 81.8 - - - +
82B PHE* 1.3 94.9 + + - +
84B GLU* 3.4 3.8 + - - +
85B VAL* 3.0 45.7 + - + +
152B VAL* 6.0 0.7 - - + -
153B ASN* 3.7 30.1 - - + -
254B HIS* 4.5 5.5 + - + +
281B ASP* 4.1 11.0 - - - +
298B GLN* 3.6 35.9 - - + -
300B THR* 3.6 30.1 - - + +
303B ILE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.5 22.0 - - + +
75B SER* 3.4 23.8 - - - -
76B ASP* 3.2 35.9 - - + +
77B ILE* 4.4 2.5 - - - +
79B ASN* 3.2 22.8 + - + -
81B PHE* 1.3 101.9 - + + +
83B ALA* 1.3 65.5 + - - +
85B VAL* 3.2 9.2 + - + +
86B ALA* 2.9 25.1 + - - +
107B GLU* 4.7 4.0 - - - -
130B ALA* 3.9 24.0 - - + -
152B VAL* 5.5 1.1 - - + -
153B ASN* 3.7 22.2 - - + -
154B ARG* 4.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.3 30.9 - - + +
78A GLU* 4.4 5.8 - - - -
83A ALA* 4.0 7.4 - - + -
77B ILE* 3.6 30.2 + - + +
79B ASN 3.2 7.8 + - - +
80B VAL* 3.9 12.6 - - + +
81B PHE 3.3 0.4 - - - -
82B PHE* 1.3 76.0 - - - +
84B GLU* 1.3 57.7 + - - +
86B ALA* 3.3 3.1 + - - +
87B SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 4.1 17.4 - - + +
80B VAL* 3.1 37.6 + - + +
81B PHE* 3.7 0.7 - - - +
83B ALA* 1.3 73.0 - - - +
85B VAL* 1.3 66.4 + - - +
87B SER* 3.5 7.0 + - - -
88B GLY 3.2 16.5 + - - -
282B ASN 5.7 0.7 - - - +
300B THR* 2.6 43.6 + - - +
301B ARG* 3.4 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 5.7 3.8 - - + -
74B VAL* 5.8 3.1 - - + -
81B PHE* 3.0 44.2 + - + +
82B PHE* 3.2 12.5 + - + +
84B GLU* 1.3 74.8 - - - +
86B ALA* 1.3 58.0 + - - +
88B GLY 3.2 2.6 + - - -
89B VAL* 3.0 28.9 + - + +
152B VAL* 4.2 25.8 - - + -
300B THR* 3.4 24.9 - - - +
303B ILE* 4.3 9.0 - - + -
304B GLY* 3.2 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 5.0 3.6 - - + -
102A LEU* 5.0 9.6 - - + +
72B LEU* 3.8 28.8 - - + +
74B VAL* 5.1 1.6 - - + -
77B ILE* 4.1 16.6 - - + -
82B PHE 2.9 16.2 + - - +
83B ALA 3.4 6.3 - - - +
85B VAL* 1.3 73.9 - - - +
87B SER* 1.3 61.8 + - - +
89B VAL* 3.3 3.6 + - - +
90B GLU* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.8 13.7 - - - +
78A GLU* 2.7 42.4 + - - -
104A ASN* 3.6 14.3 + - - +
83B ALA 3.0 8.2 + - - -
84B GLU 3.5 9.4 - - - -
86B ALA* 1.3 77.6 - - - +
88B GLY* 1.3 61.1 + - - -
90B GLU* 4.1 4.8 - - - +
91B SER* 3.0 27.9 + - - -
301B ARG* 4.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.2 10.3 + - - -
85B VAL 3.2 2.4 + - - -
87B SER* 1.3 77.9 - - - +
89B VAL* 1.3 63.4 + - - +
91B SER* 3.9 4.2 - - - -
92B GLU 3.1 17.7 + - - -
301B ARG* 3.5 28.8 - - - +
305B GLN* 3.5 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 4.3 30.1 - - + -
85B VAL* 3.0 22.0 + - + +
86B ALA* 3.3 8.7 + - - +
88B GLY* 1.3 74.1 - - - +
90B GLU* 1.3 58.5 + - - +
92B GLU* 3.4 1.7 + - - +
93B ALA* 2.9 29.3 + - - +
100B VAL* 4.5 8.3 - - + -
128B ILE* 3.8 20.0 - - + -
304B GLY* 3.4 24.4 - - - +
308B MET* 2.9 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 6.4 0.2 - - + -
102A LEU* 3.9 29.6 - - + +
103A ALA* 3.5 9.1 - - - +
104A ASN* 3.0 45.4 + - + +
111A ARG* 4.5 2.8 + - - -
72B LEU* 6.4 0.2 - - + -
86B ALA 2.8 21.0 + - - +
87B SER* 4.1 4.9 - - - +
89B VAL* 1.3 74.3 - - + +
91B SER* 1.3 65.4 + - - +
93B ALA* 4.0 0.5 - - - +
94B ARG* 3.0 54.4 + - + +
100B VAL* 4.3 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 5.7 5.1 + - - +
87B SER* 3.0 19.4 + - - -
88B GLY* 3.9 5.8 - - - -
90B GLU* 1.3 81.8 + - - +
92B GLU* 1.3 64.4 + - - +
94B ARG* 3.7 5.1 - - - +
95B HIS* 3.2 22.3 + - - +
305B GLN* 5.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 3.1 18.4 + - - +
89B VAL 3.8 2.7 - - - +
91B SER* 1.3 77.2 + - - +
93B ALA* 1.3 62.2 + - - +
95B HIS* 3.2 22.3 + - - +
96B LYS* 2.9 54.7 + - + +
305B GLN* 3.4 38.5 + - + +
308B MET* 3.8 19.5 - - + -
309B ARG* 3.4 26.0 + - + +
312B ILE* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 2.9 20.4 + - - +
90B GLU 4.0 1.3 - - - +
92B GLU* 1.3 73.2 - - - +
94B ARG* 1.3 56.6 + - - +
96B LYS* 3.1 4.5 + - - -
97B GLY 2.9 9.7 + - - -
98B TYR* 2.7 48.1 + - + +
100B VAL* 3.6 26.9 - - + -
308B MET* 3.7 18.1 - - + +
312B ILE* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 5.3 1.1 - - - +
104A ASN 3.3 19.4 + - - +
105A THR* 4.2 1.8 - - - +
111A ARG* 2.7 69.6 + - - +
114A GLU* 3.8 12.0 + - - +
115A ALA* 3.6 20.5 - - - +
118A GLN* 4.8 17.9 + - - +
90B GLU* 3.0 37.1 + - - +
91B SER* 3.7 5.8 - - - +
93B ALA* 1.3 78.4 - - - +
95B HIS* 1.3 61.6 + - - +
97B GLY* 3.2 12.5 + - - +
98B TYR 3.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER 3.2 10.1 + - - +
92B GLU* 3.2 20.2 + - - +
94B ARG* 1.3 78.1 - - - +
96B LYS* 1.3 66.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 4.5 2.9 + - - -
92B GLU* 2.9 42.7 + - - +
93B ALA 3.1 3.9 + - - +
94B ARG 3.1 0.4 - - - -
95B HIS* 1.3 85.3 - - + +
97B GLY* 1.3 61.8 + - - +
98B TYR* 3.8 14.3 + - + -
309B ARG* 3.9 15.0 + - - +
312B ILE* 3.6 46.3 - - + +
313B HIS* 5.7 5.7 + - - -
316B GLU* 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 5.0 2.3 + - - -
68B ASN* 3.5 19.7 + - - +
93B ALA 2.9 3.0 + - - -
94B ARG 3.2 11.7 + - - -
95B HIS 3.4 0.6 - - - -
96B LYS* 1.3 80.7 - - - +
98B TYR* 1.3 62.4 + - - +
99B SER* 5.4 0.3 + - - -
----------------------------------------------------------
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