Contacts of the helix formed by residues 357 - 372 (chain D) in PDB entry 2ABJ
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 357 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D PHE* 3.8 25.6 - - + -
325D GLU* 3.4 18.2 - - - +
337D PRO* 4.2 2.0 - - + -
352D THR* 3.4 25.3 - - + +
353D MET* 3.8 31.6 - - + -
355D ASN 3.3 5.6 - - - +
356D GLY* 1.3 78.2 - - - +
358D LYS* 1.3 59.4 + - - +
359D LEU 3.5 1.3 - - - -
360D ALA* 3.8 9.0 - - + -
361D SER* 3.0 29.7 + - - -
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Residues in contact with LYS 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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264D TYR* 5.8 4.3 - - + -
325D GLU* 3.1 3.9 + - - +
355D ASN 3.0 19.2 + - - +
356D GLY* 3.4 4.8 - - - -
357D PRO* 1.3 70.0 - - - +
359D LEU* 1.3 61.3 + - - +
361D SER* 3.4 6.6 + - - -
362D ARG* 2.9 30.9 + - - +
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Residues in contact with LEU 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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264D TYR* 3.6 40.1 - - + -
274D LEU* 3.7 30.1 - - + -
299D TRP* 3.8 29.2 - - + -
302D PHE* 3.9 17.9 - - + -
325D GLU* 2.7 22.9 + - - +
327D PHE* 4.1 8.3 - - + -
358D LYS* 1.3 71.0 - - - +
360D ALA* 1.3 59.7 + - - +
362D ARG* 3.2 11.4 + - - +
363D ILE* 2.9 43.3 + - + +
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Residues in contact with ALA 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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197D PHE* 4.1 5.4 - - + -
325D GLU* 2.8 21.2 + - - +
327D PHE* 4.2 17.9 - - + -
335D VAL* 3.6 27.9 - - + +
337D PRO* 4.7 5.2 - - + -
352D THR* 5.5 0.7 - - + -
357D PRO* 3.8 18.6 - - + -
358D LYS 3.4 0.2 - - - -
359D LEU* 1.3 74.1 - - - +
361D SER* 1.3 55.5 + - - +
363D ILE* 3.4 3.8 + - - +
364D LEU* 3.0 28.2 + - - +
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Residues in contact with SER 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D PHE* 3.8 19.3 - - - -
356D GLY 5.6 0.7 - - - -
357D PRO* 3.0 22.2 + - - -
358D LYS* 3.4 8.3 + - - -
360D ALA* 1.3 73.6 - - - +
362D ARG* 1.3 62.0 + - - +
364D LEU* 3.7 5.0 - - - +
365D SER* 2.9 35.4 + - - -
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Residues in contact with ARG 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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299D TRP* 3.3 58.0 - - + +
301D GLU* 2.8 43.8 + - - -
302D PHE* 5.0 4.9 - - - -
358D LYS 2.9 19.9 + - - +
359D LEU* 3.5 10.2 - - - +
361D SER* 1.3 77.5 + - - +
363D ILE* 1.3 56.9 + - - +
365D SER* 3.7 5.0 - - - -
366D LYS* 2.9 31.9 + - + +
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Residues in contact with ILE 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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274D LEU* 5.2 0.7 - - + -
292D ILE* 3.7 42.4 - - + -
295D LEU* 5.7 3.1 - - + -
299D TRP* 4.2 20.0 - - + -
327D PHE* 3.5 33.2 - - + -
335D VAL* 3.8 14.8 - - + -
359D LEU* 2.9 31.6 + - + +
360D ALA* 3.7 3.6 - - - +
362D ARG* 1.3 71.5 - - - +
364D LEU* 1.3 68.4 + - - +
366D LYS* 3.3 4.8 + - - -
367D LEU* 2.9 39.7 + - + +
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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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197D PHE* 3.6 33.4 - - + -
333D CYS 4.3 6.1 - - - +
334D VAL* 3.7 37.7 - - + -
335D VAL* 4.7 4.5 - - + +
360D ALA 3.0 17.6 + - - +
361D SER* 3.7 5.6 - - - +
363D ILE* 1.3 77.7 - - - +
365D SER* 1.3 61.1 + - - +
367D LEU* 4.1 0.5 - - - +
368D THR* 2.8 40.4 + - - +
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Residues in contact with SER 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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361D SER* 2.9 20.8 + - - -
362D ARG* 3.7 5.6 - - - -
364D LEU* 1.3 78.2 - - - +
366D LYS* 1.3 63.8 + - - +
368D THR* 3.8 3.5 - - - -
369D ASP* 2.9 38.6 + - - +
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Residues in contact with LYS 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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295D LEU* 3.9 32.3 - - + -
298D GLN* 5.7 1.8 - - - +
299D TRP* 4.3 23.7 - - + +
362D ARG* 2.9 22.3 + - + +
363D ILE* 3.3 7.2 + - - +
365D SER* 1.3 73.3 - - - +
367D LEU* 1.3 62.9 + - - +
369D ASP* 3.3 7.1 + - - +
370D ILE* 3.2 29.5 + - + +
375D GLU* 3.4 35.9 + - - +
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Residues in contact with LEU 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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109D PHE* 4.0 12.8 - - + -
288D THR* 4.0 19.5 - - + -
291D CYS* 3.9 11.2 - - + -
292D ILE* 4.3 6.5 - - + -
295D LEU* 3.8 15.7 - - + -
334D VAL* 3.7 29.2 - - + -
363D ILE* 2.9 33.6 + - + +
366D LYS* 1.3 68.9 - - - +
368D THR* 1.3 60.6 + - - +
370D ILE* 3.3 6.9 + - + +
371D GLN* 2.8 45.7 + - - +
379D TRP* 3.7 29.6 - - + -
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Residues in contact with THR 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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154D THR 4.8 4.0 - - - +
334D VAL* 4.9 3.1 - - - +
364D LEU* 2.8 39.1 + - - +
365D SER* 3.8 5.4 - - - -
367D LEU* 1.3 76.1 - - - +
369D ASP* 1.3 56.4 + - - +
371D GLN* 3.3 12.4 + - - -
372D TYR* 2.9 53.2 + - + +
374D ARG* 3.2 24.9 - - - +
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Residues in contact with ASP 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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365D SER* 2.9 31.9 + - - +
366D LYS* 3.5 8.6 - - - +
368D THR* 1.3 75.8 - - - +
370D ILE* 1.3 60.7 + - - +
373D GLY 3.3 1.9 + - - -
374D ARG* 2.8 69.4 + - + +
375D GLU* 3.3 24.2 + - + +
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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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109D PHE* 4.0 14.6 - - + -
295D LEU* 5.1 2.7 - - + -
366D LYS* 3.2 32.8 + - + +
367D LEU* 3.7 7.9 - - - +
369D ASP* 1.3 75.1 - - - +
371D GLN* 1.3 65.5 + - - +
373D GLY* 3.1 14.0 + - - -
375D GLU* 3.8 32.6 - - + +
377D SER* 3.8 29.4 - - - +
379D TRP* 3.9 29.4 - - + -
380D THR* 3.4 27.7 + - + +
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Residues in contact with GLN 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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99D PHE* 3.4 61.7 - - + +
107D ARG* 4.1 15.1 + - - +
109D PHE* 3.6 35.8 - - + -
331D THR 6.0 0.2 + - - -
334D VAL* 4.8 16.3 - - - +
367D LEU* 2.8 35.6 + - - +
368D THR* 3.7 14.3 + - - +
370D ILE* 1.3 72.5 - - - +
372D TYR* 1.3 63.2 + - + +
373D GLY 3.3 2.5 + - - -
380D THR* 4.2 7.0 - - - -
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Residues in contact with TYR 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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99D PHE* 3.7 31.5 - + + -
100D ARG 3.3 23.1 - - - -
101D GLY* 3.3 9.1 - - - -
102D VAL* 2.9 30.6 + - + +
107D ARG* 4.0 0.4 - - - -
153D SER 3.7 3.1 - - - -
154D THR* 3.2 37.9 + - + -
155D SER 3.8 1.9 - - - -
156D ALA 2.5 40.0 + - - -
157D SER* 4.2 0.9 - - - -
368D THR* 2.9 43.3 + - + +
371D GLN* 1.3 81.3 - - + +
373D GLY* 1.3 61.3 + - - +
374D ARG* 3.2 19.4 + - - +
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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