Contacts of the strand formed by residues 135 - 141 (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 LYS 135 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523 GLN* 4.5 12.1 - - - +
533 VAL 3.8 1.8 + - - -
543 TRP* 3.3 28.9 - - + +
553 LEU 3.0 23.8 + - - -
913 ASP* 3.2 22.0 + - - +
933 THR* 3.5 15.5 + - - +
1333 PHE* 3.3 3.0 - - - +
1343 ASP* 1.3 88.4 - - - +
1363 VAL* 1.3 65.1 + - - +
1373 PHE* 3.6 31.8 - - + -
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Residues in contact with VAL 136 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 TYR* 6.0 3.6 - - + -
553 LEU* 3.2 31.9 - - + +
913 ASP* 3.8 2.1 - - - +
923 ASP* 3.1 44.4 + - + +
933 THR* 3.0 14.1 + - + -
963 GLU* 3.6 41.3 - - + +
1073 MET* 5.9 0.2 - - - -
1333 PHE* 4.3 5.6 - - + -
1353 LYS* 1.3 78.8 - - - +
1373 PHE* 1.3 71.2 + - - +
1383 SER* 6.3 0.2 - - - -
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Residues in contact with PHE 137 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543 TRP* 3.8 38.4 - + - -
553 LEU 2.7 13.4 + - - +
563 ILE* 3.3 18.3 - - + -
573 LYS* 2.8 27.7 + - - +
713 PRO 5.6 5.4 - - - -
723 VAL* 5.1 15.3 - - + -
773 SER* 6.0 1.8 - - - -
893 ILE* 3.6 27.6 - - + -
903 MET 3.4 14.6 - - - +
913 ASP* 4.2 20.4 - - + -
923 ASP* 5.3 0.7 - - - -
1353 LYS* 3.6 39.0 - - + -
1363 VAL* 1.3 82.3 - - - +
1383 SER* 1.3 60.0 + - - +
1393 VAL* 4.0 0.4 - - + -
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Residues in contact with SER 138 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573 LYS* 3.4 19.5 - - - +
883 LYS 3.1 6.1 - - - +
893 ILE* 3.5 1.1 - - - -
903 MET* 3.0 43.1 + - - +
923 ASP* 3.2 27.3 + - - -
1363 VAL* 6.3 0.2 - - - -
1373 PHE* 1.3 71.9 - - - +
1393 VAL* 1.3 60.2 + - - +
1403 SER* 3.1 17.4 + - - -
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Residues in contact with VAL 139 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563 ILE* 4.3 9.9 - - + -
573 LYS* 2.8 35.9 + - - +
583 PHE* 4.0 32.8 - - + -
593 PRO* 3.3 17.7 - - + +
703 LEU* 5.6 0.2 - - + -
803 MET* 4.2 4.5 - - - -
823 ILE* 4.2 9.6 - - + -
873 TYR* 3.9 24.2 - - + -
883 LYS 3.5 3.8 - - - +
893 ILE* 3.6 31.0 - - + -
1373 PHE* 4.0 0.6 - - + -
1383 SER* 1.3 69.6 - - - +
1403 SER* 1.3 61.0 + - - +
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Residues in contact with SER 140 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573 LYS* 3.0 24.6 + - - +
593 PRO* 4.9 1.6 - - - -
873 TYR* 3.3 11.1 - - - +
883 LYS* 2.8 35.8 + - - +
903 MET* 4.3 16.1 - - - +
1383 SER* 3.1 19.3 + - - -
1393 VAL* 1.3 71.8 - - - +
1413 GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 141 (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* 5.0 5.5 - - - +
613 ASN* 5.6 3.3 + - - +
853 HIS* 3.9 23.9 - - + +
863 ASP 5.0 0.4 - - - +
873 TYR* 3.5 27.9 + - + -
883 LYS* 4.8 4.9 - - - +
1403 SER* 1.3 80.8 - - - +
1423 THR* 1.3 67.6 + - - +
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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
------------------------------------------------------------
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