Contacts of the strand formed by residues 85 - 91 (chain 3) in PDB entry 4C2M
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 85 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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813 THR* 3.2 2.2 - - - -
823 ILE 2.8 35.9 + - - +
833 ASP* 2.8 12.2 + - + +
843 LYS* 1.3 73.4 - - - +
863 ASP* 1.3 77.7 + - - +
873 TYR* 3.3 27.5 + + + +
1413 GLU* 3.9 32.6 - - + +
1423 THR 5.7 1.8 + - - -
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Residues in contact with ASP 86 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793 THR* 5.0 4.9 - - - +
803 MET 3.6 4.3 - - - +
813 THR* 3.8 20.4 - - + +
843 LYS 5.1 2.7 - - - +
853 HIS* 1.3 92.8 + - - +
873 TYR* 1.3 67.2 + - - +
1413 GLU* 5.0 0.2 - - - -
1423 THR* 3.9 30.4 + - + +
1443 LYS* 4.0 22.4 + - - -
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Residues in contact with TYR 87 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593 PRO* 3.7 20.0 - - + -
613 ASN* 4.1 8.1 + - - -
623 VAL* 3.9 20.4 - - + +
793 THR* 3.4 9.4 + - - -
803 MET* 2.7 33.8 + - + +
823 ILE* 3.9 31.4 - - + -
853 HIS* 3.3 40.8 + - - +
863 ASP* 1.3 76.4 - - - +
883 LYS* 1.3 62.9 + - - +
1393 VAL* 3.9 17.5 - - + -
1403 SER 3.3 22.7 - - - +
1413 GLU* 3.5 24.8 + - - -
1423 THR* 4.4 9.1 - - - +
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Residues in contact with LYS 88 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773 SER 5.9 3.6 - - - -
783 THR* 3.6 14.1 - - - +
793 THR* 4.5 1.1 - - - +
873 TYR* 1.3 77.5 - - - +
893 ILE* 1.3 65.3 + - - +
903 MET* 4.2 34.8 - - + +
1383 SER 3.1 4.0 - - - +
1393 VAL* 3.5 1.3 - - - -
1403 SER* 2.8 39.1 + - - +
1413 GLU 4.8 3.1 - - - +
1423 THR* 4.1 24.0 + - - +
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Residues in contact with ILE 89 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563 ILE* 6.0 0.9 - - + -
703 LEU* 4.5 9.0 - - + -
713 PRO* 3.8 30.5 - - + +
723 VAL 6.0 1.3 - - - +
773 SER* 3.7 8.1 - - - +
783 THR 2.9 36.6 + - - +
793 THR* 4.7 0.4 - - - +
803 MET* 3.5 33.4 - - + +
883 LYS* 1.3 73.0 - - - +
903 MET* 1.3 65.1 + - - +
1373 PHE* 3.6 37.2 - - + -
1383 SER 3.5 2.9 - - - +
1393 VAL* 3.6 23.6 - - + -
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Residues in contact with MET 90 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773 SER* 5.2 2.9 - - - +
883 LYS* 4.2 34.5 - - + +
893 ILE* 1.3 77.7 - - - +
913 ASP* 1.3 60.3 + - - +
923 ASP* 3.2 21.8 + - - +
1373 PHE* 3.4 9.2 - - - -
1383 SER* 3.0 57.2 + - - +
1403 SER* 4.3 15.3 - - - +
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Residues in contact with ASP 91 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773 SER* 4.3 20.3 + - - +
893 ILE 4.3 0.4 + - - -
903 MET* 1.3 68.2 - - - +
923 ASP* 1.3 59.7 + - - +
933 THR* 2.5 38.0 + - - -
943 ASP* 4.3 11.4 + - - +
1353 LYS* 3.2 24.1 + - - +
1363 VAL 3.9 3.7 - - - +
1373 PHE* 4.1 17.8 - - + -
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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