Contacts of the strand formed by residues 79 - 83 (chain 2) in PDB entry 5NET
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 79 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381 ASP* 3.8 21.6 + - - -
652 HIS 5.0 2.0 + - - -
662 LEU* 3.1 36.5 + - + +
672 PHE* 4.1 17.0 - + + -
772 ARG* 5.8 2.0 - - - +
782 CYS* 1.3 77.9 - - - +
802 LEU* 1.3 61.6 + - - +
812 LEU* 3.9 37.1 + - + +
1792 LEU 3.2 13.7 + - - +
1802 VAL* 3.3 14.0 - - - -
1812 VAL* 2.9 24.7 + - + +
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Residues in contact with LEU 80 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361 TYR* 4.4 5.4 - - - +
1371 GLY* 1.6 38.3 - - - +
1381 ASP* 2.4 53.2 + - + +
782 CYS* 3.7 27.4 - - + -
792 HIS* 1.3 79.5 + - - +
812 LEU* 1.3 61.4 + - - +
822 GLU* 4.2 1.5 + - - +
1292 LEU* 3.7 29.2 - - + +
1302 CYS* 5.3 1.1 - - - -
1312 SER 6.1 0.2 - - - +
1322 ILE* 4.4 17.7 - - + -
1782 THR* 3.9 10.1 - - + -
1792 LEU 3.7 4.5 - - - -
1802 VAL* 3.7 18.2 - - + -
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Residues in contact with LEU 81 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 THR* 4.6 15.0 - - + +
652 HIS 4.9 3.4 - - - +
662 LEU* 3.8 37.7 - - + -
792 HIS* 3.9 17.4 + - + +
802 LEU* 1.3 74.3 - - - +
822 GLU* 1.3 66.6 + - - +
832 LEU* 3.6 29.0 + - + -
852 THR* 4.9 12.8 - - + +
1782 THR* 3.6 0.9 - - - -
1792 LEU* 3.2 46.7 + - + +
2032 ILE* 5.5 1.6 - - + -
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Residues in contact with GLU 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311 ASN* 4.7 4.4 + - - -
1351 LYS 4.5 6.1 - - - +
1361 TYR* 2.1 37.3 - - - +
1371 GLY 2.5 15.9 + - - +
802 LEU 4.4 1.0 - - - +
812 LEU* 1.3 72.6 - - - +
832 LEU* 1.3 61.6 + - - +
842 PRO 3.2 16.3 - - - +
852 THR* 3.3 12.0 + - - -
1292 LEU 3.8 6.8 + - - +
1752 LYS* 3.7 34.4 + - + +
1772 TRP 3.6 4.3 - - - +
1782 THR* 2.5 37.4 + - - +
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Residues in contact with LEU 83 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 PHE* 4.9 1.6 - - + -
812 LEU* 3.6 27.3 + - + +
822 GLU* 1.3 76.5 - - - +
842 PRO* 1.3 64.8 - - + +
852 THR* 4.3 14.4 - - + +
1052 TRP* 3.9 25.4 + - + +
1072 VAL* 4.1 5.8 - - + -
1252 MET* 3.9 30.1 - - + -
1752 LYS* 3.8 5.0 - - - +
1762 PRO* 3.8 16.1 - - - +
1772 TRP* 3.1 22.7 + - + +
1792 LEU* 4.4 10.5 - - + +
2032 ILE* 4.0 34.8 - - + -
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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
------------------------------------------------------------
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