Contacts of the helix formed by residues 196 - 202 (chain 1) in PDB entry 1G6Q
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 PRO 196 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941 TYR 3.2 7.0 - - - -
1951 SER* 1.3 94.5 - - - +
1971 PHE* 1.3 59.1 + - - +
1991 PRO* 3.0 19.2 - - + +
2001 LEU 4.1 2.4 + - - -
952 MET* 3.7 23.9 - - - +
982 GLU* 3.3 34.1 - - + +
992 LEU* 3.6 23.1 - - + -
1022 LEU* 3.6 22.9 - - + -
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Residues in contact with PHE 197 (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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1861 TRP* 3.6 48.0 - + + -
1941 TYR* 2.9 36.9 + + - +
1961 PRO* 1.3 76.2 - - - +
1981 VAL* 1.3 65.7 + - - +
2001 LEU* 2.7 22.7 + - + +
2011 VAL* 2.9 21.5 + - + +
302 TYR* 3.5 26.5 - - + -
332 HIS* 4.5 4.5 - - + -
692 THR* 4.0 25.6 - - + -
922 ILE* 4.2 13.2 - - + -
952 MET* 3.8 30.7 - - + -
992 LEU* 4.4 1.8 - - + -
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Residues in contact with VAL 198 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1831 LEU* 3.9 45.4 - - + +
1861 TRP* 4.1 14.4 - - + -
1871 GLN* 4.8 8.1 - - - +
1951 SER* 3.4 15.9 - - - +
1971 PHE* 1.3 76.1 - - - +
1991 PRO* 1.3 70.7 - - + +
2011 VAL* 3.3 3.5 + - - +
2021 LEU* 3.0 32.8 + - + +
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Residues in contact with PRO 199 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1951 SER 3.6 5.8 - - - +
1961 PRO* 3.0 25.1 - - + +
1981 VAL* 1.3 91.0 - - + +
2001 LEU* 1.3 60.3 + - - +
2021 LEU* 4.4 6.3 - - + -
2031 HIS* 2.9 36.3 + - + +
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Residues in contact with LEU 200 (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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1961 PRO 4.1 1.2 + - - -
1971 PHE* 2.7 31.7 + - + +
1991 PRO* 1.3 74.0 - - - +
2011 VAL* 1.3 63.2 + - - +
2031 HIS* 3.1 13.1 + - - +
2041 GLU* 3.2 26.9 + - - +
302 TYR* 3.4 34.5 - - + +
922 ILE* 4.8 8.1 - - + -
952 MET* 4.4 19.3 - - + -
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Residues in contact with VAL 201 (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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1821 LYS* 4.3 22.7 - - + +
1831 LEU* 4.3 16.2 - - + -
1861 TRP* 3.7 22.0 - - + +
1971 PHE* 2.9 16.6 + - + +
1981 VAL 3.8 4.5 - - - +
2001 LEU* 1.3 74.7 - - - +
2021 LEU* 1.3 53.8 + - - +
2031 HIS 2.7 13.0 + - - -
2041 GLU* 2.9 18.5 + - - +
2901 TYR* 4.7 7.9 - - + -
302 TYR* 3.5 49.4 - - + +
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Residues in contact with LEU 202 (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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1791 LYS* 3.7 22.2 - - - -
1831 LEU* 4.1 17.9 - - + +
1981 VAL* 3.0 29.9 + - + +
1991 PRO* 3.8 3.8 - - + +
2011 VAL* 1.3 73.2 - - - +
2031 HIS* 1.3 83.8 + - + +
2041 GLU 3.6 1.5 - - - +
2901 TYR* 3.8 27.1 + - + +
2911 PHE 3.5 23.7 - - - +
2921 PRO* 4.4 19.3 - - + +
3451 TYR* 3.6 11.3 - - - -
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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