Contacts of the strand formed by residues 831 - 837 (chain C) in PDB entry 3D1M
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 HIS 831 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B GLU 5.2 5.2 - - - -
132B ASP 4.5 6.4 + - - -
830C PRO* 1.3 74.6 - - - +
832C ILE* 1.3 74.4 + - - +
833C ALA* 3.4 9.2 + - + -
847C TRP* 3.1 5.1 - - - +
848C THR* 2.9 47.8 + - + +
917C ASN* 3.5 28.8 + - + +
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Residues in contact with ILE 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASP 4.5 0.7 - - - +
831C HIS* 1.3 77.5 + - - +
833C ALA* 1.3 62.3 + - - +
834C TYR 3.6 21.3 - - - +
835C THR* 4.0 5.6 - - + -
845C LEU* 4.3 9.9 - - + -
846C LYS 3.6 7.9 - - - +
847C TRP* 4.1 1.1 - - + -
902C ILE* 3.7 32.3 - - + +
903C LYS* 3.8 8.1 - - - -
904C MET* 3.8 24.2 - - + -
916C SER* 3.5 21.1 - - - +
917C ASN* 2.8 33.4 + - - +
919C MET* 3.6 25.2 - - + +
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Residues in contact with ALA 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLY 4.9 5.4 - - - +
831C HIS* 3.4 14.9 + - + +
832C ILE* 1.3 75.0 - - - +
834C TYR* 1.3 67.8 + - + +
846C LYS* 2.7 34.5 + - + +
847C TRP* 4.8 0.9 - - - -
848C THR* 4.9 8.5 - - + -
919C MET* 4.2 4.8 - - - +
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Residues in contact with TYR 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832C ILE* 3.5 3.2 - - - +
833C ALA* 1.3 87.3 - - + +
835C THR* 1.3 76.3 + - - +
836C GLU* 4.5 4.0 - - + -
844C MET* 4.3 15.9 - - + +
845C LEU* 3.4 3.1 - - - -
846C LYS* 3.2 62.0 + - + +
888C TRP* 5.7 1.0 - - - +
919C MET* 3.7 8.7 - - - -
844D MET* 5.9 0.2 - - - +
846D LYS* 6.1 0.5 - - - +
888D TRP* 3.2 52.1 + + - +
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Residues in contact with THR 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 4.5 3.1 - - - +
832C ILE* 4.0 2.7 - - + -
834C TYR* 1.3 82.7 - - - +
836C GLU* 1.3 63.3 + - - +
843C ILE* 4.3 1.6 - - - -
844C MET 3.3 6.1 - - - +
845C LEU* 3.8 16.6 - - + -
902C ILE* 4.1 17.0 - - + -
919C MET* 3.7 41.0 - - + +
920C ILE 4.3 3.6 + - - -
921C CYS* 3.7 27.2 - - - +
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Residues in contact with GLU 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834C TYR* 4.5 5.8 - - + -
835C THR* 1.3 76.9 - - - +
837C ALA* 1.3 76.1 + - - +
838C VAL* 3.5 0.7 + - - +
843C ILE* 4.1 0.4 - - - +
844C MET* 2.8 39.5 + - - +
921C CYS* 3.9 6.3 - - - -
886D LYS* 3.0 36.1 + - - -
888D TRP* 3.5 28.7 + - + -
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Residues in contact with ALA 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836C GLU* 1.3 88.3 - - - +
838C VAL* 1.3 61.7 + - - +
839C SER 4.1 2.0 - - - +
842C GLN 3.6 8.3 - - - +
843C ILE* 4.1 5.6 - - + -
921C CYS* 3.6 6.8 - - - -
922C GLU 3.2 27.8 - - - +
923C THR* 3.9 13.7 - - - -
924C LYS* 4.0 24.1 - - + +
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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