Contacts of the helix formed by residues 68 - 78 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65Y CYS* 2.8 27.0 + - + +
67Y GLY* 1.3 82.4 - - - +
69Y GLU* 1.3 55.6 + - - +
70Y ALA* 3.0 5.8 - - - -
71Y CYS* 2.7 34.2 + - + +
72Y CYS* 3.8 4.4 + - - -
90Y ARG* 3.9 16.3 - - - +
194Y GLU* 3.6 20.7 - - - +
196Y ASN* 2.9 44.3 - - - +
227Y GLY 5.3 0.9 - - - -
257Y THR* 3.6 28.0 - - + +
258Y TYR 4.0 3.6 - - - +
259Y ARG* 3.5 15.8 - - + +
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Residues in contact with GLU 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Y MET* 3.7 37.7 - - + +
42Y VAL* 3.4 28.6 - - + +
43Y ARG* 2.6 53.3 + - - -
65Y CYS* 4.3 1.1 - - - +
66Y ASP* 3.1 17.1 - - - +
67Y GLY 3.1 11.4 + - - -
68Y GLN* 1.3 71.3 + - - +
70Y ALA* 1.3 61.7 + - - +
71Y CYS 3.0 1.5 + - - -
72Y CYS* 4.3 7.2 - - - -
73Y VAL* 3.2 29.3 + - + +
287Y PRO* 3.5 6.0 - - + +
288Y ILE* 4.8 1.3 - - + -
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Residues in contact with ALA 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Y MET* 4.2 8.7 - - - -
68Y GLN 2.8 1.4 + - - -
69Y GLU* 1.3 77.5 - - - +
71Y CYS* 1.3 56.8 + - - +
74Y GLY* 3.2 23.5 + - - -
227Y GLY 3.0 24.9 - - - +
228Y MET 3.6 24.0 - - - +
229Y ASP 4.1 0.4 - - - -
230Y ILE* 3.6 16.9 - - + +
233Y VAL* 3.6 11.2 - - - +
287Y PRO* 3.6 13.3 - - + +
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Residues in contact with CYS 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Y GLN* 2.7 15.3 + - + +
70Y ALA* 1.3 76.7 - - - +
72Y CYS* 1.3 61.9 + - - +
73Y VAL 3.1 0.7 - - - -
75Y LEU* 2.7 36.5 + - - +
94Y PHE* 4.9 2.5 - - + -
194Y GLU* 3.9 22.2 - - - +
227Y GLY* 3.7 23.3 - - - -
233Y VAL* 4.4 6.1 - - - -
255Y LEU* 4.0 32.8 - - + -
257Y THR* 4.4 14.4 - - - -
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Residues in contact with CYS 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y VAL* 4.6 7.2 - - - -
65Y CYS* 5.3 4.3 - - - -
68Y GLN 3.8 1.9 + - - -
69Y GLU* 4.2 13.2 - - - -
71Y CYS* 1.3 80.8 - - - +
73Y VAL* 1.3 69.2 + - - +
75Y LEU* 4.2 0.3 - - - +
76Y GLU* 3.2 23.6 + - - +
93Y GLY* 3.8 19.7 - - - -
94Y PHE* 3.3 42.3 - - + +
97Y THR* 3.6 25.0 + - + +
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Residues in contact with VAL 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y TYR* 4.2 15.9 - - + +
38Y MET* 3.7 41.1 - - + +
39Y MET* 3.8 26.9 - - + +
42Y VAL* 4.8 1.8 - - + -
69Y GLU* 3.2 18.6 + - + +
71Y CYS 3.1 0.4 - - - -
72Y CYS* 1.3 84.4 - - - +
74Y GLY* 1.3 59.2 + - - +
76Y GLU* 3.5 4.1 + - + +
77Y ALA* 2.9 27.5 + - - +
97Y THR* 4.0 14.8 - - + -
230Y ILE* 3.8 8.1 - - + -
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Residues in contact with GLY 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Y ALA 3.2 21.1 + - - -
73Y VAL* 1.3 76.0 - - - +
75Y LEU* 1.3 65.0 + - - +
77Y ALA* 3.5 4.5 + - - +
78Y GLY 3.3 7.3 + - - -
230Y ILE* 3.4 23.3 - - - +
233Y VAL* 3.7 9.2 - - - +
234Y ARG* 3.3 22.8 - - - -
237Y THR* 4.1 0.7 + - - -
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Residues in contact with LEU 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Y CYS* 2.7 20.3 + - + +
72Y CYS* 4.2 2.2 - - - +
74Y GLY* 1.3 68.8 - - - +
76Y GLU* 1.3 67.8 + - - +
78Y GLY* 2.8 14.6 + - - -
79Y ILE* 3.5 14.8 + - - +
85Y LEU* 4.7 2.2 - - + -
94Y PHE* 3.7 30.5 - - + -
162Y LEU* 3.9 25.8 - - + -
164Y LEU* 4.0 15.5 - - + -
192Y ILE* 4.2 5.8 - - + -
233Y VAL* 3.4 27.6 - - + -
237Y THR* 3.7 18.0 - - - +
253Y MET* 4.1 5.2 - - + -
255Y LEU* 3.5 20.6 - - + -
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Residues in contact with GLU 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y MET* 5.5 6.7 - - + -
72Y CYS 3.2 19.4 + - - +
73Y VAL* 3.8 6.5 - - + +
75Y LEU* 1.3 77.5 - - - +
77Y ALA* 1.3 61.1 + - - +
79Y ILE* 3.2 29.7 - - - +
80Y ASN 4.9 0.3 - - - +
81Y PRO* 4.8 6.6 - - - +
85Y LEU* 5.5 3.2 - - - +
94Y PHE* 6.0 0.7 - - - -
97Y THR* 3.3 39.9 + - - +
98Y ARG* 3.1 43.6 + - - +
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Residues in contact with ALA 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y TYR* 3.6 30.3 + - + +
73Y VAL 2.9 19.1 + - - +
74Y GLY* 3.5 10.8 - - - +
75Y LEU 3.0 0.2 - - - -
76Y GLU* 1.3 79.1 - - - +
78Y GLY* 1.3 57.2 + - - +
79Y ILE 3.4 2.0 + - - +
234Y ARG* 3.5 17.4 - - + -
238Y ARG* 2.9 22.2 + - - -
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Residues in contact with GLY 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Y GLY 3.3 3.4 + - - -
75Y LEU 2.8 8.1 + - - -
77Y ALA* 1.3 78.2 - - - +
79Y ILE* 1.3 67.6 + - - +
234Y ARG 4.0 1.8 - - - -
237Y THR* 3.7 21.8 - - - +
238Y ARG* 3.7 34.3 + - - -
241Y ALA* 4.3 5.0 - - - +
245Y ARG* 5.0 0.9 + - - -
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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