Contacts of the helix formed by residues 396 - 404 (chain D) in PDB entry 2NYM
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 GLY 396 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D LYS* 3.8 27.6 - - - +
362D ILE* 4.7 0.2 - - - +
392D ASN* 4.7 0.6 - - - -
394D VAL 3.8 1.4 + - - -
395D ILE* 1.3 83.7 - - - +
397D ILE* 1.3 61.8 + - - -
398D ARG* 2.9 15.7 + - - -
399D GLN* 3.4 10.0 + - - +
400D LEU* 3.1 17.5 + - - +
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D ASN* 4.6 14.5 + - + +
395D ILE 3.6 0.4 + - - -
396D GLY* 1.3 71.5 - - - -
398D ARG* 1.3 69.1 + - + +
400D LEU* 3.8 13.6 - - + +
401D SER* 3.0 19.4 + - - -
433D GLN* 3.6 41.3 - - + +
434D LEU* 3.7 18.6 - - + -
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Residues in contact with ARG 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D LYS* 5.9 3.1 - - - +
396D GLY* 2.9 9.4 - - - -
397D ILE* 1.3 86.6 - - + +
399D GLN* 1.3 65.7 + - + +
400D LEU 2.5 16.6 + - - -
401D SER* 2.6 20.9 + - - -
402D GLN* 2.8 23.7 + - + +
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Residues in contact with GLN 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D LYS* 5.9 1.8 - - - -
362D ILE* 3.7 29.7 - - + +
366D LEU* 3.7 13.9 - - - +
395D ILE* 4.2 10.8 - - + +
396D GLY* 3.7 18.8 - - - +
398D ARG* 1.3 86.6 - - + +
400D LEU* 1.3 56.6 + - - +
402D GLN* 3.8 18.6 - - - +
403D SER* 2.6 67.0 + - - -
404D LEU* 4.1 0.7 + - - +
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Residues in contact with LEU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D VAL* 3.7 27.1 - - + -
392D ASN* 4.2 10.8 - - + +
395D ILE* 4.1 8.3 - - + +
396D GLY 3.1 15.5 + - - +
397D ILE* 3.8 16.4 - - + +
398D ARG 2.5 4.8 + - - -
399D GLN* 1.3 70.2 - - - +
401D SER* 1.3 58.9 + - - +
402D GLN 3.0 7.6 + - - -
404D LEU* 3.1 35.5 + - + +
405D LEU* 2.9 27.1 + - + +
408D ILE* 5.2 2.2 - - + -
426D TYR* 3.8 8.7 - - - +
430D LEU* 3.6 29.6 - - + -
433D GLN* 4.0 15.3 - - - +
434D LEU* 4.8 1.3 - - + -
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Residues in contact with SER 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D ILE 3.0 10.2 + - - -
398D ARG* 2.6 20.9 + - - -
400D LEU* 1.3 77.0 - - - +
402D GLN* 1.3 57.1 + - - +
405D LEU* 3.5 27.1 - - - +
406D PRO* 4.4 1.6 - - - +
434D LEU* 3.3 35.5 - - - +
438D PHE* 3.9 15.8 - - - -
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Residues in contact with GLN 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D ARG* 2.8 23.7 + - + +
399D GLN* 4.1 19.4 - - - +
401D SER* 1.3 80.9 - - - +
403D SER* 1.3 63.5 + - - +
404D LEU 3.6 0.9 - - - -
406D PRO* 3.6 17.3 - - - +
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Residues in contact with SER 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LEU* 3.6 13.7 - - - +
370D LEU* 3.7 22.5 - - - +
399D GLN* 2.6 40.4 + - - -
402D GLN* 1.3 79.1 - - - +
404D LEU* 1.3 59.8 + - - +
406D PRO* 4.1 3.6 - - - -
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Residues in contact with LEU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LEU* 3.8 20.9 - - + -
369D PHE* 4.5 4.7 - - + -
370D LEU* 3.7 26.9 - - + -
373D LEU* 4.2 16.6 - - + +
388D LEU* 4.2 13.0 - - + -
391D VAL* 4.1 20.0 - - + -
395D ILE* 4.2 8.5 - - + -
399D GLN 4.6 0.9 - - - +
400D LEU* 3.1 37.6 + - + +
403D SER* 1.3 79.0 - - - +
405D LEU* 1.3 69.3 + - - +
406D PRO* 3.1 3.9 - - - +
407D ALA* 3.1 18.3 + - - +
408D ILE* 3.2 19.2 + - + +
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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