Contacts of the helix formed by residues 357 - 374 (chain D) in PDB entry 1OHV
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 357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C LYS* 2.8 35.1 + - - -
96D THR 4.4 4.5 - - - +
100D ARG* 3.7 20.6 + - - +
103D LEU* 4.2 2.2 - - - +
134D ALA* 6.3 0.2 - - + -
333D THR* 4.6 3.6 + - - -
356D GLY* 1.3 76.3 - - - +
358D PRO* 1.3 79.8 - - - +
359D SER* 2.9 26.9 + - - -
360D LYS* 2.9 33.9 + - + +
361D ASN* 3.3 14.3 + - - +
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Residues in contact with PRO 358 (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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96D THR* 3.7 18.8 - - + +
100D ARG* 4.9 0.7 - - + -
101D PRO* 3.7 39.3 - - + -
103D LEU* 4.0 21.3 - - + -
108D PRO* 4.3 14.1 - - + -
110D ASN* 5.8 2.5 - - - +
111D PHE* 5.4 2.5 - - + -
114D LYS* 5.2 1.0 - - - +
356D GLY 4.8 0.4 - - - +
357D ASP* 1.3 91.7 - - - +
359D SER* 1.3 54.7 + - - +
361D ASN* 3.1 14.7 + - + +
362D LEU* 2.9 28.9 + - - +
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Residues in contact with SER 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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360C LYS* 4.3 4.2 + - - -
96D THR* 3.6 21.3 - - - +
97D PHE* 3.7 33.5 - - - -
357D ASP* 2.9 32.4 + - - -
358D PRO* 1.3 77.2 - - - +
360D LYS* 1.3 71.4 + - - +
362D LEU* 3.4 5.3 - - - +
363D LEU* 3.1 28.1 + - - +
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Residues in contact with LYS 360 (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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97C PHE* 4.6 13.3 + - - +
100C ARG* 3.7 31.1 - - - +
357C ASP* 2.8 29.2 + - - -
359C SER* 4.4 4.6 + - - -
360C LYS* 5.9 0.8 - - - +
332D MET* 3.7 33.8 - - + +
333D THR* 3.9 14.4 - - - -
357D ASP* 2.9 28.6 + - + +
359D SER* 1.3 85.8 + - - +
361D ASN* 1.3 60.7 + - - +
363D LEU* 3.4 13.2 + - + +
364D LEU* 2.8 29.7 + - - +
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Residues in contact with ASN 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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103D LEU* 5.3 1.4 - - - +
111D PHE* 3.8 29.1 + - - -
114D LYS* 3.7 19.2 - - + +
115D LEU* 3.9 18.2 - - + +
118D SER* 4.3 9.0 - - - +
119D LEU* 5.5 0.9 - - - -
132D THR* 4.8 5.8 - - - +
333D THR* 3.4 26.6 + - - +
357D ASP 3.5 12.7 + - - +
358D PRO* 3.1 15.3 + - + +
360D LYS* 1.3 73.6 - - - +
362D LEU* 1.3 65.4 + - - +
364D LEU* 3.7 6.4 - - - +
365D ALA* 3.0 25.8 + - - +
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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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87D LEU* 3.6 26.7 - - + +
93D ASN* 3.6 46.4 - - + +
96D THR* 4.2 16.6 - - + +
97D PHE* 4.1 22.7 - - + -
114D LYS* 3.8 31.7 + - + +
358D PRO 2.9 13.3 + - - +
359D SER* 3.4 8.5 - - - +
361D ASN* 1.3 78.5 - - - +
363D LEU* 1.3 62.5 + - + +
365D ALA* 3.5 8.1 + - - +
366D GLU 3.7 4.5 + - - -
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Residues in contact with LEU 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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97C PHE 3.4 23.3 - - - +
98C ILE* 4.2 23.1 - - + -
84D LEU* 3.8 11.7 - - + +
87D LEU* 4.1 22.4 - - + -
88D VAL* 4.8 0.2 - - + -
97D PHE* 4.5 19.3 - - + -
332D MET* 3.8 27.1 - - + -
359D SER* 3.1 15.3 + - - +
360D LYS* 3.7 20.2 - - + +
362D LEU* 1.3 79.2 - - + +
364D LEU* 1.3 63.9 + - - +
366D GLU* 3.1 7.1 + - - +
367D VAL* 3.0 24.1 + - - +
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Residues in contact with LEU 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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118D SER* 4.0 9.0 - - - +
119D LEU* 3.8 36.1 - - + -
330D LYS 4.4 2.2 - - - +
331D MET* 3.2 46.9 - - + +
332D MET* 4.1 6.9 - - + +
333D THR* 4.2 7.6 - - + -
360D LYS 2.8 18.3 + - - +
361D ASN* 3.3 6.3 + - - +
363D LEU* 1.3 77.4 - - - +
365D ALA* 1.3 57.4 + - - +
367D VAL* 3.0 13.6 + - + +
368D ILE* 2.8 48.3 + - + +
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Residues in contact with ALA 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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114D LYS* 3.7 22.2 - - + +
117D GLU* 3.8 32.0 - - + +
118D SER* 3.8 13.9 - - - +
361D ASN 3.0 16.2 + - - +
362D LEU 3.8 4.3 - - - +
363D LEU 3.3 0.4 - - - -
364D LEU* 1.3 74.9 - - - +
366D GLU* 1.3 58.1 + - - +
368D ILE* 3.5 2.8 + - - +
369D ASN* 3.1 25.8 + - - +
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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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83D ALA* 3.9 38.0 - - + +
84D LEU* 4.0 10.1 - - + -
87D LEU* 3.6 28.1 - - + +
362D LEU 3.7 1.8 + - - +
363D LEU 3.1 9.0 + - - +
365D ALA* 1.3 78.7 - - - +
367D VAL* 1.3 65.2 + - - +
369D ASN* 3.3 26.6 + - - +
370D ILE* 3.0 29.8 + - + +
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Residues in contact with VAL 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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76D PRO* 3.7 37.5 - - + -
77D ILE* 3.9 26.4 - - + +
84D LEU* 4.2 12.3 - - + -
330D LYS 4.9 0.7 - - - +
332D MET* 4.6 7.0 - - + -
363D LEU 3.0 22.1 + - - +
364D LEU* 3.4 22.2 - - + +
366D GLU* 1.3 76.8 - - - +
368D ILE* 1.3 57.2 + - - +
370D ILE* 3.2 3.8 + - - +
371D ILE* 2.9 41.5 + - + +
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Residues in contact with ILE 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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117D GLU 4.3 7.0 - - - +
118D SER* 3.5 35.2 - - - +
119D LEU 4.2 0.4 - - - +
121D SER* 3.9 6.5 - - - +
122D VAL* 4.1 17.7 - - + -
310D PHE* 4.2 17.3 - - + -
331D MET* 4.3 2.2 - - + -
364D LEU* 2.8 37.2 + - + +
365D ALA 3.8 3.8 - - - +
367D VAL* 1.3 76.4 - - - +
369D ASN* 1.3 65.5 + - - +
371D ILE* 3.3 10.1 + - + +
372D LYS* 3.1 51.6 + - + +
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Residues in contact with ASN 369 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365D ALA 3.1 14.7 + - - +
366D GLU* 3.4 29.4 - - - +
368D ILE* 1.3 79.6 - - - +
370D ILE* 1.3 57.6 + - - +
372D LYS* 3.4 6.3 + - - +
373D ARG* 3.0 34.6 + - - +
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Residues in contact with ILE 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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77D ILE* 4.0 20.9 - - + -
81D HIS* 3.9 33.2 - - + +
83D ALA* 4.0 8.1 - - + -
366D GLU* 3.0 33.7 + - - +
367D VAL 3.2 7.2 + - - +
369D ASN* 1.3 75.5 - - - +
371D ILE* 1.3 66.0 + - - +
373D ARG* 4.5 4.9 - - + +
374D GLU* 2.9 40.7 + - + +
376D LEU* 4.1 16.4 - - + -
451D VAL* 5.9 1.6 - - + -
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Residues in contact with ILE 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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76D PRO* 5.3 0.9 - - + -
77D ILE* 4.3 4.5 - - + -
304D GLY* 4.2 2.9 - - - +
310D PHE* 3.9 28.9 - - + -
367D VAL* 2.9 34.6 + - + +
368D ILE* 3.6 9.6 - - + +
370D ILE* 1.3 74.7 - - - +
372D LYS* 1.3 63.2 + - + +
375D ASP* 3.1 4.7 + - - -
376D LEU* 2.8 47.3 + - + -
377D LEU* 4.1 31.5 + - + +
450D LEU* 3.5 30.1 - - + -
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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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121D SER* 3.3 39.9 + - - -
122D VAL* 4.3 10.7 - - - +
310D PHE* 6.1 2.2 - - - -
368D ILE* 3.1 28.2 + - + +
369D ASN* 4.0 6.3 - - - +
370D ILE 3.1 1.0 - - - -
371D ILE* 1.3 80.4 - - + +
373D ARG* 1.3 64.9 + - - +
375D ASP* 3.1 14.0 + - - +
377D LEU* 6.3 3.4 - - + -
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Residues in contact with ARG 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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369D ASN* 3.0 27.0 + - - +
370D ILE* 4.2 5.4 - - + +
372D LYS* 1.3 76.9 - - - +
374D GLU* 1.3 69.0 + - + +
375D ASP* 3.3 2.4 + - - +
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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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81D HIS* 6.2 0.2 - - - +
370D ILE* 2.9 33.7 + - + +
371D ILE 3.9 0.2 - - - -
373D ARG* 1.3 85.2 - - + +
375D ASP* 1.3 70.3 + - - +
376D LEU* 3.2 25.2 + - + +
379D ASN* 5.1 0.9 - - - +
453D ARG* 4.6 18.9 + - - +
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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