Contacts of the helix formed by residues 68 - 79 (chain S) in PDB entry 3EXG
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 68 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S CYS* 3.0 21.1 + - + +
67S GLY* 1.3 81.3 - - - +
69S GLU* 1.3 54.4 + - - +
70S ALA 3.0 6.7 - - - +
71S CYS* 2.9 32.9 + - + +
72S CYS* 3.5 7.1 + - - +
90S ARG* 3.8 17.3 - - - +
194S GLU* 3.4 30.8 - - - +
196S ASN* 3.2 14.2 + - - +
227S GLY 5.3 1.3 - - - -
257S THR* 3.4 31.3 - - - +
259S ARG* 3.1 35.2 - - + +
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Residues in contact with GLU 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S MET* 3.6 41.1 - - + +
42S VAL* 3.8 19.5 - - + -
43S ARG* 2.4 46.1 + - - +
65S CYS 4.1 0.6 + - - +
66S ASP* 3.3 11.6 - - - +
67S GLY* 2.7 27.8 + - - -
68S GLN* 1.3 70.6 - - - +
70S ALA* 1.3 56.5 + - - +
71S CYS 3.2 0.2 - - - -
72S CYS* 4.0 10.1 - - - -
73S VAL* 3.1 35.2 + - + +
287S PRO* 3.4 5.3 - - + +
288S ILE* 4.6 1.8 - - + -
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Residues in contact with ALA 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S MET* 4.1 8.3 - - - -
67S GLY 5.4 0.4 - - - +
68S GLN 3.0 0.6 - - - -
69S GLU* 1.3 78.1 - - - +
71S CYS* 1.3 57.7 + - - +
74S GLY* 3.0 26.2 + - - +
227S GLY 3.0 25.1 - - - +
228S MET 3.4 22.0 - - - +
229S ASP 4.4 0.2 - - - -
230S ILE* 4.0 15.5 - - + +
233S VAL* 3.8 8.8 - - - +
287S PRO* 3.5 14.9 - - + +
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Residues in contact with CYS 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S GLN* 2.9 21.5 + - + +
70S ALA* 1.3 76.9 - - - +
72S CYS* 1.3 61.6 + - + +
75S LEU* 2.7 39.9 + - + +
94S PHE* 5.0 0.7 - - + -
194S GLU* 3.4 23.6 - - - +
227S GLY* 4.2 13.0 - - - -
233S VAL* 4.0 2.2 - - - +
255S LEU* 3.4 38.1 - - + -
257S THR* 4.5 11.4 - - - -
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Residues in contact with CYS 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S VAL* 4.2 8.3 - - - -
65S CYS* 4.9 2.9 - - - -
68S GLN 4.1 3.6 - - - +
69S GLU* 3.9 20.0 - - - -
71S CYS* 1.3 79.8 - - + +
73S VAL* 1.3 65.8 + - - +
75S LEU* 4.3 1.3 - - - +
76S GLU* 3.5 15.2 + - - +
93S GLY* 3.7 33.9 - - - -
94S PHE* 3.6 38.1 - - + -
97S THR* 3.4 19.3 + - + +
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Residues in contact with VAL 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S TYR* 4.1 16.4 - - + +
38S MET* 3.9 32.5 - - + +
39S MET* 3.6 32.1 - - + +
42S VAL* 5.1 1.8 - - + -
69S GLU* 3.1 20.8 + - + +
72S CYS* 1.3 83.5 - - - +
74S GLY* 1.3 64.4 + - - +
76S GLU* 3.2 5.3 + - - +
77S ALA* 3.1 21.3 + - - +
97S THR* 4.4 11.9 - - + -
230S ILE* 3.7 15.9 - - + -
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Residues in contact with GLY 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S ALA 3.0 22.7 + - - -
73S VAL* 1.3 76.5 - - - +
75S LEU* 1.3 61.3 + - - +
77S ALA* 3.1 13.9 + - - +
78S GLY 3.3 8.5 + - - -
230S ILE* 3.4 15.4 - - - +
233S VAL* 3.5 18.3 - - - +
234S ARG* 3.4 12.3 - - - -
237S THR* 4.1 0.5 + - - -
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Residues in contact with LEU 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S CYS* 2.7 27.5 + - + +
72S CYS 4.3 3.4 - - - +
74S GLY* 1.3 68.5 - - - +
76S GLU* 1.3 60.3 + - - +
77S ALA 3.0 6.0 + - - -
78S GLY 3.3 6.4 + - - -
79S ILE* 3.2 23.8 + - - +
85S LEU* 5.3 0.9 - - + -
94S PHE* 3.9 22.4 - - + -
162S LEU* 3.9 21.3 - - + -
164S LEU* 4.0 16.6 - - + -
192S ILE* 4.1 7.2 - - + -
233S VAL* 3.7 7.0 - - + -
237S THR* 3.1 22.8 - - - +
253S MET* 3.6 21.8 - - + -
255S LEU* 3.9 17.9 - - + -
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Residues in contact with GLU 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S MET* 5.7 7.4 - - - -
72S CYS 3.5 14.9 + - - +
73S VAL* 3.2 7.2 + - - +
75S LEU* 1.3 77.6 - - - +
77S ALA* 1.3 60.1 + - - +
78S GLY 3.3 0.2 - - - -
79S ILE* 3.5 27.4 - - - +
80S ASN 3.8 4.7 - - - +
81S PRO* 4.9 1.9 - - - +
85S LEU* 5.7 0.9 - - - +
94S PHE* 5.7 0.9 - - - -
97S THR* 2.9 43.7 + - - +
98S ARG* 3.0 45.2 + - - +
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Residues in contact with ALA 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S TYR* 3.7 24.1 + - + +
73S VAL 3.1 10.9 + - - +
74S GLY* 3.3 7.9 - - - +
75S LEU 3.0 1.0 - - - -
76S GLU* 1.3 81.5 - - - +
78S GLY* 1.3 59.3 + - - +
79S ILE 3.4 3.3 + - - +
230S ILE* 5.1 1.3 - - + -
234S ARG* 3.3 31.2 - - + -
238S ARG* 3.1 20.4 + - - -
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Residues in contact with GLY 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S GLY 3.3 4.4 + - - -
75S LEU 3.3 3.8 + - - -
77S ALA* 1.3 79.8 - - - +
79S ILE* 1.3 58.2 + - - +
234S ARG* 3.9 2.0 - - - +
237S THR* 3.4 30.2 - - - +
238S ARG* 3.5 29.2 - - - +
241S ALA* 3.8 12.5 - - - +
245S ARG* 4.6 2.1 + - - -
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Residues in contact with ILE 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S LEU* 3.2 20.4 - - + +
76S GLU* 3.5 28.9 - - - +
77S ALA 3.4 3.7 - - - +
78S GLY* 1.3 84.2 - - - +
80S ASN* 1.3 71.4 + - - +
81S PRO* 4.9 0.2 - - - +
83S ASP* 3.8 15.7 - - + +
84S HIS 5.5 0.2 - - - +
85S LEU* 5.2 7.6 - - + -
98S ARG* 3.2 30.3 - - - +
160S VAL* 5.0 0.7 - - + -
162S LEU* 3.8 36.1 - - + -
237S THR* 3.7 12.8 - - + -
241S ALA* 4.7 7.0 - - + -
245S ARG* 4.6 3.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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