Contacts of the strand formed by residues 109 - 113 (chain 5) 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 ILE 109 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735 SER* 3.7 16.4 - - - +
745 MET* 3.7 40.2 - - + +
775 ALA* 3.8 10.8 - - + -
835 HIS* 4.5 0.2 - - - -
845 VAL* 3.4 16.4 - - + +
1005 VAL* 4.1 19.4 - - + +
1055 PHE* 3.1 33.0 + - + +
1065 SER 3.6 14.0 - - - +
1075 ASP 3.5 0.8 - - - -
1085 LYS* 1.3 83.5 - - - +
1105 THR* 1.3 63.4 + - - +
1115 LEU* 3.9 26.1 + - + +
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Residues in contact with THR 110 (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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835 HIS* 2.7 33.6 + - - -
845 VAL 2.8 10.8 + - - -
855 ILE* 3.3 11.7 - - + +
865 GLY 2.9 23.9 + - - -
1075 ASP 5.0 0.5 + - - -
1085 LYS 4.0 0.4 + - - -
1095 ILE* 1.3 72.8 - - - +
1115 LEU* 1.3 70.1 + - - +
1125 LEU* 5.0 4.9 - - + -
1225 PRO* 4.8 18.2 - - + -
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Residues in contact with LEU 111 (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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675 CYS* 4.6 11.0 - - + -
705 GLY* 5.4 4.0 - - - -
735 SER* 4.9 4.5 - - - +
865 GLY* 3.4 22.0 - - - +
935 ILE* 4.8 6.5 - - + -
965 ALA* 3.7 32.8 - - + +
975 LYS* 3.7 47.2 + - + +
1005 VAL* 4.1 14.1 - - + -
1095 ILE* 3.9 19.0 + - + +
1105 THR* 1.3 84.7 - - - +
1125 LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 112 (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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855 ILE* 4.2 15.7 - - + -
865 GLY 2.9 13.1 + - - +
875 VAL* 3.6 9.6 - - + +
885 ASP 3.4 21.3 + - - -
935 ILE* 4.0 5.5 - - - +
1105 THR* 5.0 6.3 - - + -
1115 LEU* 1.3 82.1 - - - +
1135 ARG* 1.3 61.8 + - - +
1195 VAL* 3.7 35.0 - - + +
1205 HIS* 3.5 27.1 - - + +
1215 LEU* 4.4 2.0 - - + -
1225 PRO* 3.4 34.3 - - + -
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Residues in contact with ARG 113 (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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885 ASP 3.7 5.8 - - - -
895 MET 3.4 17.0 + - - -
905 SER* 3.4 24.2 - - - +
915 SER* 3.5 30.1 - - - +
935 ILE* 3.5 22.1 - - + +
975 LYS* 5.1 6.3 - - - +
1115 LEU 4.3 0.2 + - - -
1125 LEU* 1.3 72.2 - - - +
1145 GLY* 1.3 61.7 + - - +
1195 VAL* 3.4 21.6 - - - +
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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