Contacts of the strand formed by residues 104 - 108 (chain 2) in PDB entry 1NY2
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 ALA 104 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532 LEU* 3.9 2.8 - - - -
542 THR* 2.7 38.7 + - + +
562 ALA* 3.3 19.1 - - + -
592 LEU* 3.1 36.3 - - + -
892 TYR 3.2 7.9 - - - +
902 ILE* 4.3 3.6 - - + -
1032 ILE* 1.3 76.8 - - - +
1052 LEU* 1.3 60.4 - - - +
2372 TRP* 3.9 2.7 - - - -
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Residues in contact with LEU 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 ILE* 3.7 29.8 - - + -
512 TRP* 4.0 22.0 - - + -
522 VAL 3.5 7.0 - - - +
532 LEU* 3.9 9.4 - - + -
882 ILE* 3.3 2.9 - - - +
892 TYR* 2.4 54.9 + - + +
1042 ALA* 1.3 74.6 - - - +
1062 MET* 1.3 63.1 + - - +
2372 TRP* 3.4 29.2 - - + -
2382 ILE* 3.9 20.6 - - + +
2412 VAL* 3.2 28.0 - - + -
2422 ILE* 4.7 2.5 - - + -
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Residues in contact with MET 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 LEU* 4.4 12.1 - - - -
442 ALA* 5.5 0.2 - - - -
502 ARG 3.7 1.2 - - - +
512 TRP* 3.6 8.8 - - - -
522 VAL* 2.8 59.1 + - + +
542 THR* 3.8 19.3 - - + -
592 LEU* 3.5 33.7 - - + -
662 VAL* 4.2 11.7 - - + -
852 LEU* 3.9 35.4 - - + -
872 LYS 3.3 6.5 - - - +
882 ILE* 3.7 16.2 - - + -
1052 LEU* 1.3 76.7 - - - +
1072 LYS* 1.3 61.0 + - - +
1082 LEU* 4.1 1.9 + - + +
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Residues in contact with LYS 107 (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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502 ARG* 3.0 40.2 - - - +
512 TRP* 3.8 31.8 - - + -
852 LEU* 3.6 5.4 - - - +
862 GLU* 2.6 51.2 + - + +
872 LYS* 2.7 17.1 + - + +
892 TYR* 4.3 6.3 - - + +
1062 MET* 1.3 73.8 - - - +
1082 LEU* 1.3 58.0 + - - +
2452 PHE 3.4 15.8 + - - +
2462 GLY* 3.7 18.8 - - - -
2472 GLU* 3.6 23.0 + - - -
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Residues in contact with LEU 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 LEU* 4.7 2.2 - - + -
492 ASP 3.9 1.3 - - - +
502 ARG* 2.7 57.7 + - - +
522 VAL* 3.8 21.5 - - + -
662 VAL* 3.8 20.0 - - + -
682 ILE* 5.0 0.2 - - + -
832 SER* 3.2 31.4 - - - -
842 MET 3.3 9.0 - - - +
852 LEU* 4.7 3.8 - - + -
862 GLU* 3.6 1.8 - - - -
1062 MET* 5.0 1.3 - - + +
1072 LYS* 1.3 72.2 - - - +
1092 LYS* 1.3 68.7 + - - +
1102 LYS 2.6 16.5 + - - +
1122 VAL* 3.8 25.1 - - + -
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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