Contacts of the strand formed by residues 62 - 69 (chain 2) in PDB entry 5NER
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 PHE 62 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602 ARG 4.3 6.1 - - - +
612 PHE* 1.3 76.0 - - - +
632 LYS* 1.3 74.0 + - - +
642 THR* 5.0 6.4 - - + +
832 LEU* 5.8 1.1 - - + -
852 THR* 3.6 31.6 - - + -
872 HIS* 3.5 38.6 - + + +
912 TYR* 5.3 4.0 - + - -
1052 TRP* 4.1 22.4 - + - -
2012 ALA 4.0 0.3 - - - +
2022 ASN* 3.6 1.5 - - - -
2032 ILE* 2.7 74.8 + - + +
2052 PRO* 4.1 9.0 - - + -
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Residues in contact with LYS 63 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612 PHE* 5.4 3.8 + - + +
622 PHE* 1.3 86.3 - - - +
642 THR* 1.3 65.4 + - - +
2002 TYR* 6.3 2.0 - - + -
2012 ALA 3.5 6.7 - - - +
2022 ASN* 3.7 22.9 - - + +
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Residues in contact with THR 64 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 PHE* 5.0 9.4 - - + -
632 LYS* 1.3 79.8 - - - +
652 HIS* 1.3 66.6 + - - +
662 LEU* 4.2 1.8 - - + -
812 LEU* 4.1 25.2 - - + +
852 THR* 5.8 4.3 + - + +
2002 TYR* 3.6 9.1 - - - -
2012 ALA* 2.9 52.6 + - + +
2032 ILE* 4.4 7.6 - - + -
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Residues in contact with HIS 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 THR* 1.3 82.3 + - - +
662 LEU* 1.3 67.0 + - - +
672 PHE* 3.8 26.5 + - - -
682 ASP* 3.8 23.5 + - - -
792 HIS* 4.4 3.6 + - - -
812 LEU* 6.1 0.7 - - - +
1982 LYS* 4.1 18.8 - - + -
1992 VAL 3.7 6.5 + - - -
2002 TYR* 3.3 29.7 + + + -
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Residues in contact with LEU 66 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642 THR* 3.9 7.2 - - + +
652 HIS* 1.3 86.4 - - - +
672 PHE* 1.3 71.9 + - + +
792 HIS* 3.0 41.0 - - + +
812 LEU* 4.5 10.8 - - + -
1092 VAL* 4.3 8.5 - - + -
1792 LEU* 4.5 7.4 - - + -
1812 VAL* 3.6 31.2 - - + -
1992 VAL* 2.8 32.3 + - + +
2002 TYR 4.6 0.7 - - - -
2012 ALA* 3.4 34.3 - - + +
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Residues in contact with PHE 67 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381 GLU* 4.2 7.2 - - - +
652 HIS* 3.8 9.7 + - - -
662 LEU* 1.3 86.7 - - + +
682 ASP* 1.3 73.8 + - - +
692 TRP* 3.9 25.4 - + + -
772 ARG* 3.0 35.0 - - - +
792 HIS* 3.5 19.7 - - + -
1212 LEU* 4.1 11.0 - - + -
1812 VAL* 3.5 44.2 - - + -
1832 VAL* 4.7 7.2 - - + -
1982 LYS* 3.8 0.7 - - - -
1992 VAL* 2.9 43.8 + - + +
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Residues in contact with ASP 68 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652 HIS* 3.8 10.9 + - - -
672 PHE* 1.3 82.2 - - - +
692 TRP* 1.3 60.6 + - - +
702 VAL* 3.4 12.9 + - + +
732 ASP* 3.5 8.5 - - - +
772 ARG* 4.8 2.8 + - - -
1962 GLN* 3.9 26.0 + - - +
1972 ILE 3.7 4.3 - - - +
1982 LYS* 3.0 33.8 - - - +
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Residues in contact with TRP 69 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672 PHE* 3.8 14.8 + + + -
682 ASP* 1.3 68.4 - - - +
702 VAL* 1.3 67.6 + - - +
732 ASP* 4.2 5.6 + - + -
1112 ALA* 5.1 1.3 - - + -
1182 GLY 3.9 1.6 - - - -
1192 GLY 3.7 6.7 - - - -
1202 CYS* 3.6 23.3 - - - -
1212 LEU* 3.9 31.4 - - + -
1482 ILE* 5.1 1.6 - - + -
1502 PRO* 4.1 16.6 - - + -
1832 VAL* 3.8 29.2 - - + +
1852 ALA 3.7 20.6 - - - -
1872 LEU* 3.2 49.0 - - + +
1972 ILE* 2.7 65.7 + - + +
1992 VAL* 4.3 6.7 - - + -
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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