Contacts of the helix formed by residues 367 - 377 (chain D) in PDB entry 1YAA
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 PRO 367 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365D LEU 4.4 1.3 - - - +
366D THR* 1.3 87.5 - - + +
368D GLN* 1.3 76.0 + - - +
370D VAL* 3.9 5.0 - - + +
371D LYS* 3.0 28.2 + - - +
383D ALA* 3.8 29.6 - - + +
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Residues in contact with GLN 368 (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 THR* 3.0 19.6 + - - +
367D PRO* 1.3 106.1 - - - +
369D MET* 1.3 63.6 + - - +
371D LYS* 3.7 8.7 - - + +
372D ARG* 2.9 24.1 + - - +
411D TYR* 3.4 38.8 + - + +
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Residues in contact with MET 369 (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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364D GLY 5.4 0.7 - - - +
365D LEU* 3.8 28.0 - - + -
366D THR* 2.9 36.2 + - + +
368D GLN* 1.3 78.0 - - - +
370D VAL* 1.3 56.3 + - - +
372D ARG* 3.3 2.8 + - - +
373D LEU* 2.9 34.5 + - - +
407D VAL* 3.8 14.7 - - + +
408D VAL* 3.8 32.3 - - + +
411D TYR* 3.7 43.5 - - + +
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Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D LEU* 4.0 12.1 - - + +
366D THR 2.9 18.6 + - - +
367D PRO* 3.9 7.0 - - + +
369D MET* 1.3 75.7 - - - +
371D LYS* 1.3 63.7 + - - +
373D LEU* 3.1 20.1 + - - +
374D GLU* 3.2 13.9 + - + +
379D VAL 4.6 0.7 - - - +
381D LEU* 4.1 24.0 - - + +
382D VAL 3.5 30.1 - - - +
383D ALA* 3.9 14.4 - - + +
385D GLY* 3.9 18.6 - - - +
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Residues in contact with LYS 371 (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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367D PRO 3.0 20.6 + - - +
368D GLN* 3.7 8.1 - - - +
369D MET 3.4 0.2 - - - -
370D VAL* 1.3 76.6 - - - +
372D ARG* 1.3 62.5 + - - +
374D GLU* 3.5 8.6 + - + +
375D GLU* 3.1 53.0 + - - +
411D TYR* 6.1 1.3 - - - +
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Residues in contact with ARG 372 (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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368D GLN 2.9 18.5 + - - +
369D MET 3.7 4.3 - - - +
371D LYS* 1.3 74.5 - - - +
373D LEU* 1.3 58.5 + - - +
375D GLU* 4.4 7.2 - - - -
376D THR* 2.8 64.2 + - - +
377D HIS* 4.3 0.3 - - - -
406D GLU* 2.7 37.1 + - - -
407D VAL* 3.7 14.4 - - + -
410D PHE* 3.6 39.3 - - - -
411D TYR* 3.5 28.8 + - + +
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Residues in contact with LEU 373 (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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365D LEU* 3.7 30.7 - - + -
369D MET 2.9 20.1 + - - +
370D VAL* 3.1 12.1 + - - +
372D ARG* 1.3 77.2 - - - +
374D GLU* 1.3 56.8 + - - +
377D HIS* 2.9 28.6 + - + +
378D ALA 3.0 7.3 + - - -
379D VAL* 3.0 25.8 + - + +
381D LEU* 3.9 15.7 - - + -
403D ALA* 3.7 44.2 - - + +
404D ILE* 3.9 11.2 - - + +
407D VAL* 3.8 11.4 - - + -
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Residues in contact with GLU 374 (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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23D ARG* 2.9 48.6 + - - +
29D ARG* 2.8 32.7 + - - +
370D VAL* 3.2 10.5 + - + +
371D LYS* 4.0 9.5 - - + +
373D LEU* 1.3 78.2 - - - +
375D GLU* 1.3 63.7 + - + +
378D ALA* 3.2 5.9 + - - +
379D VAL 3.3 20.2 - - - +
380D TYR* 3.5 27.0 + - + +
381D LEU 5.4 2.2 - - - +
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Residues in contact with GLU 375 (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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29D ARG* 2.9 20.2 + - - +
371D LYS* 3.1 45.1 + - - +
372D ARG* 4.0 5.2 - - - +
374D GLU* 1.3 85.2 - - + +
376D THR* 1.3 61.6 + - - +
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Residues in contact with THR 376 (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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29D ARG* 4.1 6.3 + - - -
372D ARG* 2.8 54.6 + - - +
375D GLU* 1.3 78.8 - - - +
377D HIS* 1.3 82.8 + - + +
378D ALA 3.6 0.7 - - - -
406D GLU* 5.3 0.4 - - - -
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Residues in contact with HIS 377 (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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31D THR* 5.0 0.7 - - - -
373D LEU* 2.9 18.4 + - + +
376D THR* 1.3 96.5 + - + +
378D ALA* 1.3 70.3 + - - +
379D VAL* 3.2 8.8 + - + +
399D TYR* 2.8 33.3 + - - +
402D LYS 5.3 0.2 - - - -
403D ALA* 3.6 39.8 + - + +
406D GLU* 2.8 46.1 + - + +
407D VAL* 4.1 10.3 - - + -
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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