Contacts of the helix formed by residues 68 - 79 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G CYS* 2.8 23.9 + - + +
67G GLY* 1.3 81.7 - - - +
69G GLU* 1.3 57.7 + - - +
70G ALA* 2.8 13.4 + - - -
71G CYS* 2.8 24.9 + - + +
72G CYS* 4.1 3.1 + - - -
90G ARG* 3.5 23.4 - - - +
194G GLU* 3.3 26.5 - - - +
196G ASN* 3.1 30.0 - - - +
227G GLY 5.2 1.3 - - - -
257G THR* 3.6 26.2 - - + +
258G TYR 4.4 1.1 - - - +
259G ARG* 3.4 18.2 - - + +
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Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G MET* 3.7 38.6 - - + +
42G VAL* 3.6 26.1 - - + +
43G ARG* 2.6 52.9 + - - -
65G CYS* 4.2 1.6 - - - +
66G ASP* 3.1 17.2 - - - +
67G GLY 3.6 3.8 - - - -
68G GLN* 1.3 73.3 + - - +
70G ALA* 1.3 57.3 + - - +
71G CYS 2.9 10.1 + - - -
72G CYS* 4.3 9.9 - - - -
73G VAL* 3.2 25.9 + - + +
287G PRO* 3.4 5.6 - - + +
288G ILE* 4.7 0.7 - - + -
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G MET* 4.2 8.5 - - - -
68G GLN 2.8 1.4 + - - -
69G GLU* 1.3 78.4 - - - +
71G CYS* 1.3 59.4 + - - +
74G GLY* 3.3 17.4 + - - +
227G GLY 3.3 24.7 - - - +
228G MET 3.8 12.1 - - - +
229G ASP 4.1 0.4 - - - -
230G ILE* 3.7 27.3 - - + +
233G VAL* 3.3 16.1 - - - +
287G PRO* 3.8 12.2 - - + +
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Residues in contact with CYS 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLN* 2.8 21.6 + - + +
69G GLU 2.9 1.8 - - - -
70G ALA* 1.3 81.7 - - - +
72G CYS* 1.3 61.4 + - - +
73G VAL 3.1 0.9 - - - -
75G LEU* 2.8 39.9 + - + +
94G PHE* 5.0 1.3 - - + -
194G GLU* 4.8 15.5 - - - +
227G GLY* 4.2 13.5 - - - -
233G VAL* 4.3 4.7 - - - -
255G LEU* 3.7 37.5 - - + -
257G THR* 4.7 10.5 - - - -
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Residues in contact with CYS 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G VAL* 4.9 4.9 - - - -
65G CYS* 5.1 4.5 - - - -
68G GLN 4.5 2.5 - - - -
69G GLU* 4.2 18.6 - - - -
71G CYS* 1.3 77.2 - - - +
73G VAL* 1.3 65.3 + - - +
75G LEU* 3.6 1.4 - - - +
76G GLU* 2.7 30.3 + - - +
93G GLY* 3.9 22.0 - - - -
94G PHE* 3.6 38.6 - - + +
97G THR* 3.4 23.0 + - + -
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Residues in contact with VAL 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G TYR* 4.2 18.4 - - + +
38G MET* 3.9 34.5 - - + +
39G MET* 3.7 24.7 - - + +
42G VAL* 5.1 2.2 - - + -
69G GLU* 3.2 20.8 + - + +
71G CYS 3.1 0.4 - - - -
72G CYS* 1.3 85.0 - - - +
74G GLY* 1.3 65.7 + - - +
76G GLU* 3.7 4.7 - - + +
77G ALA* 2.9 23.4 + - - +
97G THR* 4.2 10.5 - - + -
230G ILE* 3.7 12.3 - - + -
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Residues in contact with GLY 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ALA 3.3 17.9 + - - -
73G VAL* 1.3 78.6 - - - +
75G LEU* 1.3 59.8 + - - +
77G ALA* 3.2 7.4 + - - +
78G GLY* 3.1 15.8 + - - -
230G ILE* 3.2 26.6 - - - +
233G VAL* 3.5 15.0 - - - -
234G ARG* 3.4 10.2 - - - -
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Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G CYS* 2.8 19.7 + - + +
72G CYS* 3.6 4.0 - - - +
74G GLY* 1.3 75.2 - - - +
76G GLU* 1.3 59.4 + - - +
78G GLY* 3.0 13.2 + - - -
79G ILE* 3.4 22.4 - - - +
85G LEU* 5.0 2.9 - - + -
94G PHE* 3.7 30.7 - - + -
162G LEU* 3.9 19.1 - - + -
164G LEU* 4.0 17.3 - - + -
192G ILE* 4.5 4.7 - - + -
233G VAL* 3.3 26.0 - - + +
237G THR* 3.4 17.3 - - - +
253G MET* 3.9 16.8 - - + -
255G LEU* 3.9 11.4 - - + -
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Residues in contact with GLU 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LYS* 6.3 0.2 - - - -
38G MET* 5.6 6.7 - - + -
72G CYS 2.7 20.9 + - - +
73G VAL* 3.2 7.2 + - + +
75G LEU* 1.3 74.2 - - - +
77G ALA* 1.3 61.2 + - - +
79G ILE* 3.1 33.7 - - - +
81G PRO* 4.4 5.4 - - - +
85G LEU* 5.3 2.9 - - - +
94G PHE* 6.0 0.2 - - - -
97G THR* 3.3 36.6 + - - +
98G ARG* 2.7 49.0 + - - -
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Residues in contact with ALA 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LYS* 5.8 3.1 - - - +
35G TYR* 3.3 39.6 + - + +
73G VAL 2.9 12.4 + - - +
74G GLY* 3.3 13.0 - - - +
75G LEU 3.2 0.2 - - - -
76G GLU* 1.3 78.7 - - - +
78G GLY* 1.3 59.1 + - - +
79G ILE 3.3 0.8 + - - +
230G ILE* 5.1 0.4 - - + -
234G ARG* 3.6 12.3 - - + -
238G ARG* 3.7 19.6 + - - -
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Residues in contact with GLY 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G GLY 3.1 6.4 + - - -
75G LEU 3.0 5.9 + - - -
77G ALA* 1.3 78.2 - - - +
79G ILE* 1.3 66.0 + - - +
234G ARG 4.2 1.3 - - - -
237G THR* 3.4 26.7 - - - +
238G ARG* 3.9 28.9 - - - +
241G ALA* 4.4 5.9 - - - +
245G ARG* 5.0 1.6 + - - -
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Residues in contact with ILE 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU 3.4 14.6 - - - +
76G GLU* 3.1 32.9 - - - +
77G ALA 3.3 1.8 + - - -
78G GLY* 1.3 86.8 - - - +
80G ASN* 1.3 68.3 + - - +
81G PRO* 3.9 2.6 - - - +
83G ASP* 3.3 26.9 - - + +
84G HIS 5.3 0.2 - - - +
85G LEU* 4.4 13.7 - - + -
98G ARG* 4.1 16.2 - - - +
162G LEU* 3.9 32.5 - - + -
237G THR* 3.4 20.9 - - + -
241G ALA* 4.8 6.5 - - + -
245G ARG* 4.7 1.8 - - - +
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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