Contacts of the helix formed by residues 519 - 526 (chain A) in PDB entry 3NYN
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 GLU 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 4.8 17.8 + - + +
26A LYS* 5.7 1.3 - - - +
515A MET 4.0 0.4 - - - -
516A VAL 3.3 12.4 + - - +
517A GLU 3.2 9.8 - - - +
518A THR* 1.3 77.9 - - - +
520A CYS* 1.3 62.5 + - - +
521A PHE 3.3 2.5 - - - +
522A GLN* 4.1 11.6 - - + +
523A GLU* 3.0 27.7 + - + +
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Residues in contact with CYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 4.2 11.2 - - - -
30A TRP* 3.8 29.4 - - + -
34A LEU* 4.2 14.1 - - + -
173A TRP* 4.0 3.1 - - + -
208A THR* 4.3 10.1 - - - -
515A MET* 3.0 20.5 + - - +
518A THR* 2.7 36.7 + - - +
519A GLU* 1.3 70.8 - - - +
521A PHE* 1.3 64.5 + - - +
523A GLU* 4.4 3.6 - - - -
524A LEU* 2.9 30.5 + - + +
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Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.9 22.7 - - + -
65A LEU* 3.7 39.7 - - + -
66A LEU* 4.4 9.2 - - + -
69A GLU* 3.7 17.0 - - - -
173A TRP* 3.6 33.1 - + + -
515A MET* 3.1 18.7 + - + +
516A VAL* 4.1 19.5 - - + -
520A CYS* 1.3 76.8 - - - +
522A GLN* 1.3 67.3 + - + +
525A ASN* 2.6 72.4 + - + +
532B SER 5.2 1.3 - - - -
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Residues in contact with GLN 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 4.1 4.9 - - - +
516A VAL* 5.8 0.2 - - - +
519A GLU* 3.7 15.1 + - + +
521A PHE* 1.3 89.6 - - + +
523A GLU* 1.3 67.2 + - - +
525A ASN* 4.6 2.3 + - - -
526A VAL* 3.4 25.6 + - + +
528B GLY 3.0 26.3 + - - +
529B LEU* 4.3 15.6 - - - +
532B SER* 3.1 29.4 + - - +
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 3.7 20.2 - - + -
31A ARG* 2.9 37.3 + - - +
519A GLU* 3.0 21.3 + - + +
520A CYS 3.9 2.5 - - - +
522A GLN* 1.3 81.5 - - - +
524A LEU* 1.3 59.7 + - - +
526A VAL* 4.2 11.4 - - - +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 3.9 23.3 - - + -
31A ARG* 4.0 34.1 - - + +
34A LEU* 3.5 45.1 - - + +
36A PHE* 3.8 14.4 - - + -
169A ARG* 3.7 7.4 + - - -
173A TRP* 4.3 14.4 - - + -
520A CYS 2.9 18.0 + - - +
523A GLU* 1.3 78.7 - - - +
525A ASN* 1.3 66.9 + - - +
526A VAL 3.3 8.1 + - - +
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Residues in contact with ASN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.5 0.4 - - - -
66A LEU* 4.0 4.9 - - - +
69A GLU* 3.4 22.8 + - - -
169A ARG* 2.7 64.7 + - - +
173A TRP* 3.0 13.8 + - - +
521A PHE* 2.6 62.6 + - + +
522A GLN* 4.3 2.2 + - - +
524A LEU* 1.3 73.1 - - - +
526A VAL* 1.3 57.9 + - - +
527A PHE* 4.0 0.9 - - - +
527B PHE* 4.5 5.5 - - - -
528B GLY* 4.6 5.1 + - - -
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Residues in contact with VAL 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ARG* 3.6 0.5 + - - -
522A GLN* 3.4 19.0 + - - +
523A GLU* 4.2 9.3 - - - +
524A LEU 3.4 8.5 - - - +
525A ASN* 1.3 84.6 - - - +
527A PHE* 1.3 67.5 + - - +
529A LEU* 4.2 21.8 - - + +
530A ASP* 6.1 2.0 - - - +
166B TYR* 5.1 0.5 + - - -
526B VAL* 5.6 0.4 - - + -
527B PHE 3.3 17.0 - - - +
528B GLY* 3.4 28.3 - - - +
529B LEU* 3.8 21.1 - - + +
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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