Contacts of the helix formed by residues 68 - 78 (chain 1) 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 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651 CYS* 3.1 23.5 + - + +
671 GLY* 1.3 81.7 - - - +
691 GLU* 1.3 54.2 + - - +
701 ALA* 3.0 4.7 - - - -
711 CYS* 2.7 39.0 + - + +
721 CYS* 4.0 3.4 + - - -
901 ARG* 3.8 15.2 - - - +
1941 GLU* 3.2 31.3 - - - +
1961 ASN* 3.2 18.5 + - - +
2271 GLY 5.7 0.4 - - - -
2571 THR* 3.4 24.2 + - - +
2591 ARG* 3.2 37.3 - - + +
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Residues in contact with GLU 69 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 MET* 3.6 41.1 - - + +
421 VAL* 3.7 20.4 - - + +
431 ARG* 2.5 52.6 + - - -
651 CYS* 4.2 1.8 + - - +
661 ASP* 3.5 12.6 - - - +
671 GLY 2.9 20.4 + - - -
681 GLN* 1.3 77.5 + - - +
701 ALA* 1.3 61.0 - - - +
711 CYS 3.1 0.9 + - - -
721 CYS* 3.6 8.5 + - - -
731 VAL* 3.1 31.2 + - + +
2871 PRO* 3.5 5.5 - - + +
2881 ILE* 5.1 0.7 - - + -
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Residues in contact with ALA 70 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 MET* 4.3 9.8 - - - -
671 GLY 5.6 0.2 - - - +
681 GLN 2.9 1.5 + - - +
691 GLU* 1.3 77.8 - - - +
711 CYS* 1.3 57.4 + - - +
741 GLY* 3.1 20.5 + - - -
2271 GLY 2.8 27.4 - - - +
2281 MET 3.6 18.2 - - - +
2291 ASP 4.2 0.4 - - - -
2301 ILE* 3.7 18.0 - - + +
2331 VAL* 3.2 13.9 - - + +
2871 PRO* 4.0 11.9 - - + +
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Residues in contact with CYS 71 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681 GLN* 2.7 20.9 + - + +
701 ALA* 1.3 76.9 - - - +
721 CYS* 1.3 60.1 + - - +
751 LEU* 2.9 37.5 + - + +
941 PHE* 4.6 4.5 - - + -
1941 GLU* 4.7 15.9 - - + +
2271 GLY* 4.0 20.2 - - - -
2331 VAL* 4.2 5.4 - - - -
2551 LEU* 3.5 35.7 - - + -
2571 THR* 4.5 15.0 - - - -
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Residues in contact with CYS 72 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421 VAL* 4.8 5.8 - - - -
651 CYS* 5.4 3.1 - - - -
681 GLN 4.8 1.8 - - - -
691 GLU* 4.0 15.9 - - - -
711 CYS* 1.3 78.3 - - - +
731 VAL* 1.3 70.5 + - - +
751 LEU* 4.3 0.6 - - - +
761 GLU* 3.2 23.4 + - - +
931 GLY* 3.9 27.8 - - - -
941 PHE* 3.6 42.0 - - + -
971 THR* 3.6 17.7 + - - +
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Residues in contact with VAL 73 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 TYR* 3.9 29.4 - - + +
381 MET* 4.2 24.1 - - + +
391 MET* 3.5 29.8 - - + +
421 VAL* 5.6 1.6 - - + -
691 GLU* 3.1 19.8 + - + +
721 CYS* 1.3 86.4 - - - +
741 GLY* 1.3 57.7 + - - +
761 GLU* 3.4 4.3 + - - +
771 ALA* 3.1 25.1 + - - +
971 THR* 4.3 11.9 - - + -
2301 ILE* 3.9 11.2 - - + -
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Residues in contact with GLY 74 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701 ALA 3.1 15.9 + - - -
731 VAL* 1.3 77.0 - - - +
751 LEU* 1.3 62.2 + - - +
771 ALA* 3.2 11.9 + - - +
781 GLY 3.3 9.0 + - - -
2301 ILE* 3.3 24.7 - - - +
2331 VAL* 3.6 11.7 - - - -
2341 ARG* 3.3 14.8 - - - -
2371 THR* 4.1 0.7 + - - -
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Residues in contact with LEU 75 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711 CYS 2.9 25.4 + - - +
721 CYS* 4.3 3.4 - - - +
741 GLY* 1.3 73.6 - - - +
761 GLU* 1.3 65.2 + - - +
781 GLY 3.2 9.4 + - - -
791 ILE* 3.3 23.9 + - - +
851 LEU* 4.7 2.2 - - + -
941 PHE* 3.9 11.9 - - + -
1621 LEU* 3.9 19.3 - - + -
1641 LEU* 3.9 24.2 - - + -
1921 ILE* 3.7 17.5 - - + -
2331 VAL* 3.6 13.1 - - + +
2371 THR* 3.1 22.5 - - - +
2531 MET* 3.8 17.9 - - + -
2551 LEU* 4.0 10.8 - - + -
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Residues in contact with GLU 76 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 MET* 6.0 7.0 - - + -
721 CYS 3.2 18.0 + - - +
731 VAL* 3.7 5.4 - - - +
751 LEU* 1.3 80.7 - - - +
771 ALA* 1.3 56.4 + - - +
791 ILE* 3.1 28.3 - - - +
801 ASN 4.3 5.7 - - - +
811 PRO* 4.7 5.2 - - - +
851 LEU* 5.4 3.5 - - - +
941 PHE* 5.8 1.0 - - - -
971 THR* 3.2 35.9 + - - +
981 ARG* 3.0 46.0 + - - +
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Residues in contact with ALA 77 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 TYR* 3.1 42.6 + - + +
731 VAL 3.1 10.8 + - - +
741 GLY* 3.4 8.3 - - - +
751 LEU 3.2 1.0 - - - -
761 GLU* 1.3 75.9 - - - +
781 GLY* 1.3 59.3 + - - +
791 ILE 3.5 1.7 + - - +
2341 ARG* 3.3 19.3 - - + -
2381 ARG* 3.7 15.6 + - - -
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Residues in contact with GLY 78 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 GLY 3.3 5.5 + - - -
751 LEU 3.2 4.4 + - - -
771 ALA* 1.3 79.1 - - - +
791 ILE* 1.3 67.2 + - - +
2341 ARG 4.2 2.0 - - - -
2371 THR* 3.4 20.7 - - - +
2381 ARG* 3.6 29.1 - - - +
2411 ALA* 3.9 12.6 - - - +
2451 ARG* 4.7 1.6 + - - -
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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