Contacts of the helix formed by residues 68 - 77 (chain 5) 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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655 CYS* 3.0 30.7 + - + +
675 GLY* 1.3 79.8 - - - +
695 GLU* 1.3 54.0 + - - -
705 ALA 2.9 6.7 - - - +
715 CYS* 2.8 27.0 + - - +
725 CYS* 3.6 7.4 + - - -
905 ARG* 4.2 9.8 - - - +
945 PHE* 5.8 1.6 - - - -
1945 GLU* 3.6 27.8 + - - +
1965 ASN* 2.8 33.7 - - - +
2275 GLY 5.2 0.2 - - - -
2575 THR* 3.4 27.1 - - + +
2585 TYR 4.4 1.3 - - - +
2595 ARG* 3.4 25.7 - - + +
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Residues in contact with GLU 69 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395 MET* 3.6 37.2 - - + +
425 VAL* 3.5 26.4 - - + -
435 ARG* 2.7 49.5 + - - +
655 CYS 4.5 0.4 - - - +
665 ASP* 3.3 8.4 - - - -
675 GLY 2.9 20.2 + - - -
685 GLN* 1.3 70.6 - - - +
705 ALA* 1.3 61.3 + - - +
715 CYS 3.1 0.8 + - - -
725 CYS* 4.1 10.1 - - - -
735 VAL* 3.3 28.0 + - + +
2875 PRO* 3.4 8.2 - - + +
2885 ILE* 4.6 2.0 - - + -
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Residues in contact with ALA 70 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 MET* 4.2 6.7 - - - -
675 GLY 4.8 0.4 - - - +
685 GLN 2.9 0.8 - - - -
695 GLU* 1.3 80.6 - - - +
715 CYS* 1.3 57.3 + - - +
745 GLY* 3.2 22.7 + - - -
2275 GLY 3.1 25.6 - - - +
2285 MET 3.7 11.2 - - - +
2295 ASP 3.9 0.7 - - - +
2305 ILE* 3.7 14.8 - - + +
2335 VAL* 3.5 11.0 - - - +
2875 PRO* 3.5 26.6 - - + +
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Residues in contact with CYS 71 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685 GLN* 2.8 13.1 + - - +
705 ALA* 1.3 77.2 - - - +
725 CYS* 1.3 55.6 + - - +
745 GLY 3.0 1.2 + - - -
755 LEU* 2.6 42.9 + - + +
945 PHE* 4.8 2.5 - - + -
1945 GLU* 3.6 23.3 - - - +
2275 GLY* 3.7 22.4 - - - -
2335 VAL* 4.3 5.8 - - - -
2555 LEU* 3.5 33.2 - - + -
2575 THR* 4.2 13.2 - - - -
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Residues in contact with CYS 72 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425 VAL* 4.7 5.6 - - - -
655 CYS* 5.1 3.6 - - - -
685 GLN 4.0 12.1 - - - -
695 GLU* 4.1 11.2 - - - -
715 CYS* 1.3 80.7 - - - +
735 VAL* 1.3 66.0 + - - +
755 LEU* 4.0 0.8 - - - +
765 GLU* 3.1 23.9 + - - +
935 GLY* 4.0 24.9 - - - +
945 PHE* 3.5 44.8 - - + -
975 THR* 3.5 17.2 + - + +
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Residues in contact with VAL 73 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 TYR* 4.1 19.3 - - + +
385 MET* 4.0 28.3 - - + +
395 MET* 3.6 32.3 - - + +
425 VAL* 5.2 1.3 - - + -
695 GLU* 3.3 19.8 + - + +
715 CYS 3.3 0.6 - - - -
725 CYS* 1.3 80.8 - - - +
745 GLY* 1.3 66.0 + - - +
765 GLU* 3.3 4.7 + - - +
775 ALA* 3.2 22.0 + - - +
975 THR* 4.1 17.5 - - + -
2305 ILE* 3.7 12.3 - - + +
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Residues in contact with GLY 74 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705 ALA 3.2 14.3 + - - -
715 CYS 3.0 3.8 + - - -
735 VAL* 1.3 77.1 - - - +
755 LEU* 1.3 61.9 + - - +
775 ALA* 3.5 9.1 + - - -
785 GLY 3.5 2.9 + - - -
2305 ILE* 3.2 27.3 - - - +
2335 VAL* 3.7 11.7 - - - -
2345 ARG* 3.4 22.0 - - - +
2375 THR* 4.2 0.5 + - - -
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Residues in contact with LEU 75 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715 CYS 2.6 15.0 + - - +
725 CYS* 4.0 4.5 - - - +
745 GLY* 1.3 76.2 - - - +
765 GLU* 1.3 60.2 + - - +
785 GLY* 2.8 20.1 + - - -
795 ILE* 3.4 14.1 + - - +
855 LEU* 4.3 3.4 - - + -
945 PHE* 3.7 28.3 - - + -
1625 LEU* 3.9 21.8 - - + -
1645 LEU* 4.0 16.6 - - + -
1925 ILE* 4.2 10.5 - - + -
2335 VAL* 3.5 19.3 - - + -
2375 THR* 3.4 24.3 - - - +
2535 MET* 4.2 10.8 - - + -
2555 LEU* 4.1 16.6 - - + -
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Residues in contact with GLU 76 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385 MET* 5.7 7.0 - - + -
725 CYS 3.1 18.0 + - - +
735 VAL* 3.3 4.7 + - - +
755 LEU* 1.3 78.7 - - - +
775 ALA* 1.3 57.2 + - - +
795 ILE* 3.1 32.1 - - - +
805 ASN 4.5 0.3 - - - +
815 PRO* 4.4 10.4 - - - +
855 LEU* 5.3 4.1 - - - +
975 THR* 3.3 34.3 + - - +
985 ARG* 2.8 45.4 + - - -
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Residues in contact with ALA 77 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345 LYS* 5.7 3.1 - - - +
355 TYR* 3.4 40.2 - - + +
735 VAL 3.2 13.7 + - - +
745 GLY* 3.5 5.6 + - - +
755 LEU 3.0 1.2 + - - -
765 GLU* 1.3 75.7 - - - +
785 GLY* 1.3 58.9 + - - +
795 ILE 3.5 1.1 - - - -
2305 ILE* 6.2 0.2 - - + -
2345 ARG* 3.6 10.1 - - + +
2385 ARG* 3.6 21.1 + - - -
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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