Contacts of the helix formed by residues 358 - 373 (chain D) in PDB entry 2OQH
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 ASP 358 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334D ILE* 2.7 15.5 + - - +
335D ILE* 5.5 0.9 - - - -
356D SER 3.7 2.9 + - - +
357D VAL* 1.3 69.9 - - - +
359D GLU* 1.3 57.3 + - - +
360D ASP* 3.0 22.5 + - - +
361D LYS* 3.1 43.0 + - + +
362D LEU* 3.0 24.6 + - - +
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Residues in contact with GLU 359 (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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11D TRP* 5.9 1.0 - - + -
37D ARG* 3.6 22.2 + - - -
45D GLU* 3.8 13.5 - - - +
47D TRP* 3.8 31.7 - - + -
357D VAL* 3.2 8.4 + - + +
358D ASP* 1.3 69.3 + - - +
360D ASP* 1.3 62.5 + - - +
362D LEU* 3.5 12.6 - - + +
363D ARG* 3.1 30.3 + - - +
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Residues in contact with ASP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D ASP* 3.0 10.3 + - - +
359D GLU* 1.3 76.2 - - - +
361D LYS* 1.3 68.8 + - + +
363D ARG* 2.9 33.3 + - - +
364D HIS* 2.9 23.8 + - - +
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Residues in contact with LYS 361 (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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153C GLU* 6.3 3.1 - - - -
157C ARG* 5.7 7.3 - - - +
332D ASP* 2.6 40.8 + - - +
333D ASP 3.3 17.0 + - - +
334D ILE* 4.1 10.1 - - + -
335D ILE 5.0 3.2 + - - -
336D GLU* 5.0 9.3 + - - -
358D ASP* 3.1 40.1 + - + +
360D ASP* 1.3 79.3 - - + +
362D LEU* 1.3 57.1 + - - +
364D HIS* 3.3 7.4 + - + +
365D TYR* 2.9 43.1 + - + -
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Residues in contact with LEU 362 (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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11D TRP* 3.7 33.4 - - + +
13D VAL* 3.9 21.5 - - + +
35D VAL* 4.1 11.2 - - + -
47D TRP* 3.4 37.7 - - + -
334D ILE* 3.8 28.7 - - + +
357D VAL* 4.5 3.4 - - + -
358D ASP 3.0 13.6 + - - +
359D GLU* 3.5 15.3 - - + +
360D ASP 3.1 0.2 - - - -
361D LYS* 1.3 78.5 - - - +
363D ARG* 1.3 62.5 + - + +
365D TYR* 3.4 1.0 + - - -
366D ALA* 3.0 23.6 + - - +
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Residues in contact with ARG 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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11D TRP* 5.2 10.8 - - + +
359D GLU 3.1 15.5 + - - +
360D ASP* 2.9 35.0 + - - +
362D LEU* 1.3 75.0 - - + +
364D HIS* 1.3 59.0 + - - +
366D ALA* 3.1 9.0 + - - +
367D GLY* 2.8 26.7 + - - -
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Residues in contact with HIS 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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146C ASP* 5.1 10.8 + - + +
149C LYS* 3.9 41.8 + - + -
150C ALA* 6.4 0.2 - - - -
360D ASP 2.9 13.8 + - - +
361D LYS* 3.3 11.2 - - + +
363D ARG* 1.3 79.4 - - - +
365D TYR* 1.3 95.5 + + - +
367D GLY* 2.9 18.1 + - - -
368D VAL* 2.9 31.4 + - + +
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Residues in contact with TYR 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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150C ALA* 6.1 0.5 - - - +
13D VAL* 3.9 17.7 - - + -
14D ASN 3.1 41.9 + - - +
15D LEU* 3.3 19.3 - - + -
16D PRO* 3.7 22.8 - - + +
332D ASP* 2.5 43.1 + - + +
333D ASP 4.9 2.0 - - - -
334D ILE* 4.1 6.5 - - + -
361D LYS* 2.9 40.9 + - + +
362D LEU 4.9 0.2 - - - -
364D HIS* 1.3 98.9 + + - +
366D ALA* 1.3 56.5 + - - +
367D GLY 3.2 0.2 - - - -
368D VAL* 3.5 9.7 + - + +
369D ASN 3.2 13.0 + - - -
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Residues in contact with ALA 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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11D TRP* 4.2 20.9 - - + -
12D VAL 3.5 19.2 - - - +
13D VAL* 3.8 6.0 - - + +
362D LEU 3.0 17.7 + - - +
363D ARG* 3.1 6.7 + - - +
365D TYR* 1.3 74.9 - - - +
367D GLY* 1.3 62.6 + - - +
369D ASN* 3.3 3.1 + - - +
370D GLU* 3.0 26.9 + - - +
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Residues in contact with GLY 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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363D ARG 2.8 13.7 + - - -
364D HIS* 2.9 5.5 + - - -
366D ALA* 1.3 78.4 - - - +
368D VAL* 1.3 61.0 + - - +
370D GLU* 3.1 10.8 + - - +
371D ARG* 3.0 23.2 + - - +
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Residues in contact with VAL 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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146C ASP* 4.6 10.1 - - - +
14D ASN* 3.8 21.0 + - + +
364D HIS* 2.9 41.5 + - + +
365D TYR* 3.6 16.6 - - + +
367D GLY* 1.3 77.8 - - - +
369D ASN* 1.3 56.7 + - - +
371D ARG* 3.3 21.9 + - - +
372D ASP* 3.0 44.7 + - - +
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Residues in contact with ASN 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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12D VAL* 3.2 47.9 - - - +
14D ASN* 3.0 35.1 + - - +
32D THR* 3.9 0.8 + - - -
365D TYR 3.2 10.2 + - - +
366D ALA 3.7 1.7 - - - +
367D GLY 3.2 0.4 - - - -
368D VAL* 1.3 74.1 - - - +
370D GLU* 1.3 63.3 + - - +
373D GLY* 2.7 35.1 + - - -
374D ASP* 3.1 25.9 + - - +
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Residues in contact with GLU 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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366D ALA 3.0 12.7 + - - +
367D GLY* 3.3 13.2 - - - +
369D ASN* 1.3 82.8 + - - +
371D ARG* 1.3 60.0 + - - +
373D GLY* 4.4 1.7 + - - -
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Residues in contact with ARG 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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143C THR* 4.4 4.6 + - - +
145C ALA* 4.9 11.9 + - - +
146C ASP* 2.6 44.2 + - - -
367D GLY 3.0 15.0 + - - +
368D VAL* 3.7 14.9 - - - +
369D ASN 3.2 0.2 - - - -
370D GLU* 1.3 81.4 - - + +
372D ASP* 1.3 88.0 + - - +
373D GLY 3.5 0.2 - - - -
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Residues in contact with ASP 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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143C THR* 5.4 6.3 - - - +
146C ASP* 5.0 0.3 - - - +
14D ASN* 3.9 11.3 + - - +
368D VAL* 3.0 23.8 + - - +
371D ARG* 1.3 112.0 + - - +
373D GLY* 1.3 63.1 + - - +
374D ASP 4.5 2.4 - - - +
375D LEU* 4.7 11.5 - - + +
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Residues in contact with GLY 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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14D ASN* 3.0 18.9 + - - -
369D ASN* 2.7 27.9 + - - -
370D GLU 4.4 1.9 + - - -
371D ARG 3.5 1.8 + - - -
372D ASP* 1.3 79.3 - - - +
374D ASP* 1.3 66.8 + - - -
375D LEU* 3.6 1.4 + - - +
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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