Contacts of the helix formed by residues 68 - 77 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65I CYS* 3.0 28.1 + - + +
67I GLY* 1.3 81.7 - - - +
69I GLU* 1.3 56.7 + - - +
70I ALA* 3.1 3.4 - - - -
71I CYS* 2.9 33.9 + - + +
72I CYS* 3.7 5.4 + - - -
90I ARG* 3.8 19.0 - - - +
194I GLU* 3.6 26.1 - - - +
196I ASN* 4.3 8.9 + - - -
227I GLY 5.5 0.9 - - - -
257I THR* 3.3 31.0 - - + +
259I ARG* 3.0 43.3 - - - +
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Residues in contact with GLU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I MET* 3.8 32.4 - - + +
42I VAL* 3.5 28.3 - - + -
43I ARG* 2.6 58.2 + - - -
65I CYS 4.3 1.6 - - - +
66I ASP* 3.3 12.9 - - - -
67I GLY* 2.9 20.5 + - - -
68I GLN* 1.3 75.1 - - - +
70I ALA* 1.3 64.5 + - - +
71I CYS 3.0 2.1 + - - -
72I CYS* 4.2 7.0 - - - -
73I VAL* 3.1 28.3 + - + +
287I PRO* 3.7 5.9 - - + +
288I ILE* 4.8 1.1 - - + -
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I MET* 4.2 9.2 - - - -
67I GLY 5.7 0.2 - - - +
68I GLN 3.1 0.6 + - - -
69I GLU* 1.3 77.7 - - - +
71I CYS* 1.3 56.7 + - - +
74I GLY* 2.7 29.5 + - - -
227I GLY 3.0 28.9 - - - +
228I MET* 3.3 24.0 - - - +
229I ASP 4.2 0.2 - - - -
230I ILE* 3.9 15.7 - - + +
233I VAL* 3.4 7.8 - - + +
287I PRO* 4.0 8.6 - - + +
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Residues in contact with CYS 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I GLN* 2.9 17.9 + - + +
70I ALA* 1.3 77.2 - - - +
72I CYS* 1.3 60.0 + - - +
75I LEU* 2.9 35.7 + - - +
94I PHE* 4.5 6.1 - - + -
194I GLU* 4.4 19.3 - - - +
227I GLY* 3.9 18.6 - - - -
233I VAL* 4.2 5.4 - - - -
255I LEU* 3.6 38.4 - - + -
257I THR* 4.8 9.6 - - - -
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Residues in contact with CYS 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I VAL* 4.5 8.7 - - - -
65I CYS* 5.4 3.6 - - - -
68I GLN 4.5 1.8 - - - -
69I GLU* 4.1 18.8 - - - -
71I CYS* 1.3 79.9 - - - +
73I VAL* 1.3 63.6 + - - +
75I LEU* 4.4 0.5 - - - +
76I GLU* 3.2 26.9 + - - +
93I GLY* 3.9 18.6 - - - -
94I PHE* 3.6 42.6 - - + +
97I THR* 3.4 25.3 + - + -
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Residues in contact with VAL 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I TYR* 4.3 18.7 - - + +
38I MET* 3.8 35.4 - - + +
39I MET* 3.7 24.2 - - + +
42I VAL* 5.2 1.8 - - + -
69I GLU* 3.1 19.6 + - + +
71I CYS 3.3 0.2 - - - -
72I CYS* 1.3 83.5 - - - +
74I GLY* 1.3 65.2 + - - +
76I GLU* 3.4 4.7 + - - +
77I ALA* 3.1 21.1 + - - +
97I THR* 4.2 9.0 - - + -
230I ILE* 3.9 13.0 - - + -
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Residues in contact with GLY 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ALA 2.7 25.7 + - - -
73I VAL* 1.3 75.8 - - - +
75I LEU* 1.3 56.8 + - - +
77I ALA* 3.1 21.6 + - - +
78I GLY* 3.4 2.3 + - - -
230I ILE* 3.3 20.4 - - - +
233I VAL* 3.5 12.3 - - - -
234I ARG* 3.3 15.1 - - - -
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I CYS 2.9 18.9 + - - +
72I CYS 4.4 2.0 - - - +
74I GLY* 1.3 72.0 - - - +
76I GLU* 1.3 66.0 - - - +
77I ALA 3.0 1.6 - - - -
78I GLY* 3.0 12.0 + - - -
79I ILE* 3.4 16.7 + - + +
85I LEU* 4.7 1.8 - - + -
94I PHE* 4.1 25.6 - - + -
162I LEU* 3.8 19.1 - - + -
164I LEU* 4.2 5.8 - - + -
192I ILE* 3.6 22.7 - - + -
233I VAL* 3.5 20.5 - - + +
237I THR* 3.1 31.5 - - - +
253I MET* 3.6 16.6 - - + -
255I LEU* 4.0 15.3 - - + -
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Residues in contact with GLU 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I MET* 5.5 7.6 - - + -
72I CYS 3.2 18.4 + - - +
73I VAL* 3.5 8.5 - - + +
75I LEU* 1.3 80.6 - - - +
77I ALA* 1.3 54.7 + - - +
78I GLY 3.3 0.2 - - - -
79I ILE* 3.4 25.3 - - - +
80I ASN 4.6 2.4 - - - +
81I PRO* 5.1 1.2 - - - +
85I LEU* 5.9 0.7 - - - +
94I PHE* 5.7 1.0 - - - -
97I THR* 3.2 40.9 + - - +
98I ARG* 3.1 40.8 + - - +
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Residues in contact with ALA 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I TYR* 3.4 30.2 + - + +
73I VAL 3.1 11.8 + - - +
74I GLY* 3.1 13.6 + - - +
75I LEU 3.0 1.4 - - - -
76I GLU* 1.3 79.2 - - - +
78I GLY* 1.3 56.3 + - - +
79I ILE 3.5 1.7 + - - -
230I ILE* 5.5 0.2 - - + -
234I ARG* 3.4 18.6 - - + -
238I ARG* 2.8 26.0 + - - -
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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