Contacts of the helix formed by residues 362 - 377 (chain D) in PDB entry 2WQI
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 ARG 362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353C ASP* 4.2 7.3 + - - +
355C TYR* 3.3 51.5 + - + +
361D GLY* 1.3 68.3 - - - -
363D GLU* 1.3 63.8 + - + +
365D PHE* 3.1 4.6 + - + +
366D GLU* 2.8 56.6 + - + +
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Residues in contact with GLU 363 (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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361D GLY 3.4 0.2 - - - -
362D ARG* 1.3 78.2 - - + +
364D ASN* 1.3 65.7 + - - +
366D GLU* 3.3 11.8 + - - +
367D ILE* 3.0 34.9 + - + +
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Residues in contact with ASN 364 (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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375C LEU* 3.6 47.1 + - + +
376C GLU* 4.5 2.8 - - - +
379C GLU* 2.9 28.8 + - - +
359D VAL* 3.9 11.4 - - + -
360D ARG 3.0 20.5 + - - +
361D GLY* 3.2 9.6 + - - +
362D ARG 3.2 0.8 - - - -
363D GLU* 1.3 77.4 - - - +
365D PHE* 1.3 65.2 + - - +
367D ILE* 3.3 6.5 + - - +
368D LEU* 3.0 29.7 + - - +
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Residues in contact with PHE 365 (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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355C TYR* 3.3 48.9 - + + -
356C TYR 3.6 27.6 - - - -
357C LEU* 4.3 5.4 - - + -
359D VAL* 3.8 17.9 - - + +
361D GLY 2.9 14.2 + - - +
362D ARG* 3.1 8.0 + - + +
364D ASN* 1.3 74.6 - - - +
366D GLU* 1.3 70.7 + - + +
368D LEU* 3.3 2.5 + - - -
369D MET* 2.8 61.8 + - + +
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Residues in contact with GLU 366 (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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362D ARG* 2.8 54.2 + - - +
363D GLU* 3.9 10.1 - - - +
364D ASN 3.2 0.2 - - - -
365D PHE* 1.3 87.1 - - + +
367D ILE* 1.3 62.9 + - + +
369D MET* 3.4 6.6 + - + +
370D LYS* 3.1 40.0 + - - +
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Residues in contact with ILE 367 (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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367A ILE* 4.7 14.8 - - + +
370A LYS* 3.6 31.0 - - + -
371A LEU* 3.9 26.9 - - + -
375C LEU* 4.3 16.8 - - + -
363D GLU* 3.0 27.9 + - + +
364D ASN* 3.6 6.5 - - - +
366D GLU* 1.3 76.8 - - + +
368D LEU* 1.3 63.9 + - - +
370D LYS* 3.2 14.5 + - + +
371D LEU* 3.1 32.4 + - + +
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Residues in contact with LEU 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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357C LEU* 3.8 16.7 - - + +
368C LEU* 3.9 25.2 - - + +
371C LEU* 3.9 28.0 - - + -
372C LYS* 4.1 16.4 - - + +
375C LEU* 4.1 11.7 - - + -
357D LEU* 4.4 7.4 - - + -
359D VAL* 3.7 34.3 - - + -
364D ASN 3.0 20.5 + - - +
365D PHE* 3.8 3.4 - - - +
367D ILE* 1.3 75.2 - - - +
369D MET* 1.3 57.9 + - - +
371D LEU* 3.3 9.3 + - + +
372D LYS* 2.8 30.3 + - - +
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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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356C TYR 5.3 0.2 - - - +
357C LEU* 3.8 23.1 - - + -
358C GLN 5.6 0.2 - - - -
365D PHE* 2.8 59.7 + - + +
366D GLU* 3.7 8.1 - - + +
367D ILE 3.2 0.2 - - - -
368D LEU* 1.3 75.5 - - - +
370D LYS* 1.3 61.3 + - + +
372D LYS* 3.5 25.2 + - + +
373D GLU* 3.0 25.0 + - + +
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Residues in contact with LYS 370 (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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367A ILE* 4.4 31.6 - - + +
375B LEU* 4.9 4.2 - - + +
378B MET* 5.1 1.4 - - - +
366D GLU* 3.1 27.4 + - - +
367D ILE* 3.2 13.0 + - - +
369D MET* 1.3 75.9 - - + +
371D LEU* 1.3 60.4 + - + +
373D GLU* 3.4 9.5 + - - +
374D SER* 3.0 28.3 + - - -
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Residues in contact with LEU 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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367A ILE* 4.1 19.7 - - + -
371A LEU* 3.5 28.0 - - + -
371B LEU* 4.0 20.2 - - + -
375B LEU* 4.3 21.3 - - + -
368C LEU* 3.9 9.4 - - + -
371C LEU* 3.5 22.7 - - + -
367D ILE* 3.1 26.0 + - + +
368D LEU* 3.7 10.3 - - + +
370D LYS* 1.3 74.6 - - + +
372D LYS* 1.3 65.4 + - - +
374D SER* 3.0 5.7 + - - +
375D LEU* 2.9 31.1 + - - +
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Residues in contact with LYS 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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389B TYR* 3.7 9.9 - - - -
393B GLN* 3.1 28.1 + - - +
357C LEU* 4.2 6.3 - - + -
358C GLN* 2.8 32.2 + - - +
359C VAL* 4.2 5.8 - - + +
368C LEU* 4.0 21.9 - - + +
368D LEU 2.8 20.4 + - - +
369D MET* 3.7 36.1 - - + +
371D LEU* 1.3 71.5 - - - +
373D GLU* 1.3 65.1 + - - +
375D LEU* 3.4 3.9 + - - +
376D GLU* 3.0 54.8 + - - +
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Residues in contact with GLU 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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378B MET* 3.2 11.6 - - + +
389B TYR* 3.7 22.3 - - + +
390B ARG* 2.6 54.9 + - - +
369D MET* 3.0 19.0 + - + +
370D LYS* 3.5 8.7 - - - +
371D LEU 3.2 0.2 - - - -
372D LYS* 1.3 80.6 - - + +
374D SER* 1.3 57.9 + - - +
376D GLU* 3.3 1.0 + - - +
377D LEU* 2.8 48.0 + - + +
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Residues in contact with SER 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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374B SER* 2.7 40.2 + - - +
375B LEU* 3.9 14.6 - - - +
378B MET* 3.8 22.2 - - - +
370D LYS 3.0 16.2 + - - -
371D LEU* 3.0 17.2 + - - +
373D GLU* 1.3 76.3 - - - +
375D LEU* 1.3 55.7 + - - +
378D MET* 2.9 33.4 + - - +
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Residues in contact with LEU 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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370B LYS* 3.8 29.6 - - + -
371B LEU* 4.3 14.4 - - + -
374B SER* 3.8 22.7 - - - +
364C ASN* 3.5 36.8 + - + +
367C ILE* 4.3 8.7 - - + -
368C LEU* 4.1 24.2 - - + -
371D LEU 2.9 25.8 + - - +
372D LYS* 3.7 5.4 - - - +
374D SER* 1.3 77.3 + - - +
376D GLU* 1.3 62.0 + - + +
378D MET* 3.5 13.6 - - - +
379D GLU* 3.6 14.7 - - - +
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Residues in contact with GLU 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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389B TYR* 2.6 45.3 + - + +
393B GLN* 3.5 3.8 + - - -
359C VAL* 3.5 5.4 - - + +
360C ARG* 2.8 48.3 + - + +
364C ASN* 4.3 4.5 - - - +
372D LYS* 3.0 42.4 + - - +
373D GLU 3.9 0.2 - - - +
375D LEU* 1.3 76.1 - - + +
377D LEU* 1.3 66.3 + - - +
379D GLU* 3.3 27.9 + - - +
380D LEU* 4.3 5.7 + - - +
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Residues in contact with LEU 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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378B MET* 3.4 37.0 - - + -
381B VAL* 3.7 13.0 - - + +
386B VAL* 4.4 26.2 - - + -
389B TYR* 3.5 36.8 - - + -
373D GLU* 2.8 47.2 + - + +
376D GLU* 1.3 69.4 - - - +
378D MET* 1.3 57.8 + - - +
379D GLU 2.9 5.4 - - - -
380D LEU* 2.8 47.1 + - + +
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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