Contacts of the strand formed by residues 828 - 833 (chain A) in PDB entry 5ID6
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 VAL 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A PRO 4.3 0.4 - - - +
827A TYR* 1.3 80.6 - - - +
829A ILE* 1.3 64.1 + - - +
830A GLY 3.6 0.3 + - - -
842A VAL 3.5 1.7 - - - +
843A VAL* 3.5 3.9 - - - -
844A VAL* 3.0 39.7 + - + +
920A ALA* 4.4 0.2 - - - -
921A VAL* 3.5 12.6 - - + +
923A ALA* 3.9 19.7 - - + -
1188A ALA* 3.9 23.9 - - + +
1191A VAL* 4.0 21.3 - - + -
1192A LEU* 3.7 31.4 - - + -
1195A ILE* 4.1 8.1 - - + -
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Residues in contact with ILE 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A VAL* 1.3 72.2 - - - +
830A GLY* 1.3 59.5 + - - +
831A ILE* 3.8 13.1 + - + -
841A ILE* 3.8 27.6 - - + -
842A VAL 3.7 2.7 - - - -
843A VAL* 4.4 14.6 - - + +
911A ILE* 4.3 6.3 - - + +
914A LEU* 3.5 20.4 - - + +
915A VAL* 3.5 46.9 - - + +
920A ALA* 3.7 15.9 - - + +
921A VAL 2.8 10.7 + - - +
922A ILE* 3.6 7.9 - - + +
923A ALA 2.7 31.2 + - - +
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Residues in contact with GLY 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A VAL 3.6 2.0 + - - -
829A ILE* 1.3 71.2 - - - +
831A ILE* 1.3 61.4 + - - +
841A ILE* 3.2 9.2 - - - +
842A VAL 2.7 39.3 + - - -
923A ALA* 3.8 6.7 - - - -
1184A ALA* 3.6 23.4 - - - +
1187A ILE* 4.6 0.4 - - - -
1188A ALA* 3.9 10.1 - - - +
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Residues in contact with ILE 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A ILE* 4.5 5.8 - - + +
830A GLY* 1.3 76.5 - - - -
832A ASP* 1.3 65.3 + - - +
839A LEU* 4.0 23.3 - - + -
840A TYR 3.5 6.5 - - - +
841A ILE* 3.7 19.5 - - + -
907A VAL* 6.1 0.2 - - + -
911A ILE* 4.0 26.7 - - + -
922A ILE* 4.0 17.9 - - + -
923A ALA 3.1 13.2 + - - +
924A LEU* 3.6 28.4 - - + +
925A GLU* 4.6 2.1 + - - +
943A TYR* 3.5 19.7 + - - +
946A PHE* 4.5 11.4 - - + -
950A LEU* 4.9 0.9 - - + -
1184A ALA* 4.3 1.3 - - - -
1187A ILE* 4.0 12.5 - - - +
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Residues in contact with ASP 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A ILE* 1.3 75.4 - - - +
833A ARG* 1.3 79.0 + - - +
834A GLY* 5.4 0.5 - - - -
839A LEU* 3.4 7.0 - - - +
840A TYR* 2.9 33.7 + - + +
925A GLU* 5.0 7.8 - - - +
943A TYR* 4.7 2.0 - - - -
998A ALA* 5.5 2.3 - - - +
1001A THR* 5.3 0.7 + - - -
1002A SER* 4.4 6.1 + - - -
1180A ASP* 4.0 8.9 - - - +
1183A GLY* 3.5 19.8 - - - -
1184A ALA* 3.5 23.0 + - + +
1187A ILE* 3.6 19.7 - - + +
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Residues in contact with ARG 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A ASP* 1.3 92.1 + - - +
834A GLY* 1.3 60.2 + - - +
838A LEU 3.6 8.1 - - - +
839A LEU* 3.6 21.8 - - + -
925A GLU* 2.8 27.9 + - - -
927A LEU* 3.6 4.4 - - - +
931A PHE 4.7 0.2 + - - -
932A LYS* 3.2 50.3 - - - +
936A VAL* 3.8 22.0 - - + +
938A VAL* 2.8 35.1 + - + +
939A GLU 3.8 1.0 + - - -
940A LYS* 3.7 7.1 - - - +
943A TYR* 3.6 36.4 + - + +
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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