Contacts of the helix formed by residues 315 - 330 (chain D) in PDB entry 1JIQ
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 ASN 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.0 1.1 - - - -
81D ARG* 4.3 2.6 + - - -
306D HIS* 3.7 5.5 - - - +
307D PHE* 2.9 36.5 - - - +
310D THR* 3.0 21.5 - - - +
311D PRO 3.3 9.2 + - - +
312D LEU* 3.2 15.3 + - - +
313D GLU 3.7 0.2 - - - -
314D LYS* 1.3 73.3 - - - +
316D ALA* 1.3 66.6 + - - +
317D PRO* 3.1 29.5 - - - +
318D VAL* 3.2 19.1 + - + +
319D LEU* 3.0 23.3 + - - +
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.6 21.6 - - + +
44D LEU* 4.0 15.3 - - + -
53D VAL* 4.4 11.2 - - + +
306D HIS* 3.0 18.4 + - - +
315D ASN* 1.3 70.7 - - - +
317D PRO* 1.3 69.4 - - + +
319D LEU* 3.2 3.7 + - - +
320D LEU* 3.0 28.0 + - - +
493D MET* 4.1 17.3 - - + -
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Residues in contact with PRO 317 (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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303D MET* 4.4 5.6 - - - -
306D HIS* 3.8 9.4 - - + -
307D PHE* 3.7 23.1 - - + -
315D ASN* 3.1 20.0 - - - +
316D ALA* 1.3 95.6 - - + +
318D VAL* 1.3 54.4 + - - +
320D LEU* 3.5 1.9 + - + -
321D ALA* 2.9 29.5 + - - +
493D MET* 3.5 35.2 - - + +
496D HIS* 3.7 15.9 - - + -
497D LYS* 3.6 12.7 - - + +
500D VAL* 4.9 0.9 - - - -
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Residues in contact with VAL 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA* 4.7 7.2 - - + -
77D VAL* 4.7 3.1 - - + -
307D PHE* 3.8 18.4 - - + -
312D LEU* 3.9 37.2 - - + +
315D ASN* 3.2 34.0 + - + +
317D PRO* 1.3 75.3 - - - +
319D LEU* 1.3 60.8 + - - +
321D ALA* 3.2 7.2 + - - +
322D LEU* 2.9 49.0 + - + +
500D VAL* 4.1 11.7 - - + -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 4.3 15.3 - - + -
53D VAL* 6.2 2.0 - - + -
55D TYR* 3.6 41.5 - - + +
65D MET* 4.1 20.7 - - + +
69D VAL* 4.6 10.3 - - + -
312D LEU 3.7 17.0 - - - +
313D GLU* 3.6 24.0 - - - +
315D ASN 3.0 19.4 + - - +
316D ALA* 3.7 4.3 - - - +
318D VAL* 1.3 77.5 - - - +
320D LEU* 1.3 64.3 + - + +
322D LEU* 3.2 9.1 + - + +
323D LEU* 2.9 31.5 + - + +
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Residues in contact with LEU 320 (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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53D VAL* 4.0 22.4 - - + -
55D TYR* 5.7 0.4 - - + -
316D ALA 3.0 19.6 + - - +
317D PRO* 3.8 5.2 - - + +
319D LEU* 1.3 75.6 - - + +
321D ALA* 1.3 62.9 + - - +
323D LEU* 3.4 8.2 + - + +
324D GLY 3.1 16.8 + - - -
405D ASP* 5.1 3.6 - - - +
475D ASN* 3.6 29.7 - - - +
477D ILE* 4.2 11.9 - - + -
493D MET* 3.7 40.2 - - + -
494D TYR* 4.8 11.0 - - + -
497D LYS* 3.9 25.3 + - + +
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Residues in contact with ALA 321 (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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317D PRO 2.9 18.2 + - - +
318D VAL 3.3 6.1 - - - +
320D LEU* 1.3 76.2 - - - +
322D LEU* 1.3 58.4 + - - +
324D GLY 3.1 0.9 + - - -
325D ILE* 3.0 29.2 + - - +
497D LYS* 3.6 20.4 - - - +
500D VAL* 3.4 33.2 - - + -
501D GLN* 3.1 17.0 - - + +
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Residues in contact with LEU 322 (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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65D MET* 5.4 2.9 - - + -
68D LEU* 3.4 61.1 - - + +
69D VAL* 3.9 15.3 - - + +
71D LEU* 4.7 5.8 - - + -
72D ALA* 4.2 6.3 - - + +
318D VAL* 2.9 40.4 + - + +
319D LEU* 3.8 8.7 - - + +
321D ALA* 1.3 75.5 - - + +
323D LEU* 1.3 65.8 + - - +
325D ILE* 3.1 7.0 + - + +
326D TRP* 2.9 22.5 + - - +
500D VAL* 5.3 0.4 - - + -
504D ILE* 3.6 29.6 - - + -
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Residues in contact with LEU 323 (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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55D TYR* 3.6 33.7 - - + -
58D ASN* 3.6 31.6 - - + +
60D VAL* 3.9 20.6 - - + -
65D MET* 4.6 14.1 - - + -
68D LEU* 5.0 1.1 - - + -
319D LEU* 2.9 25.4 + - + +
320D LEU* 3.7 9.9 - - + +
322D LEU* 1.3 74.7 - - - +
324D GLY* 1.3 62.4 + - - +
326D TRP* 3.2 7.6 + - + +
327D TYR* 3.1 37.4 + - + -
475D ASN* 3.6 20.0 - - - +
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Residues in contact with GLY 324 (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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320D LEU 3.1 9.1 + - - -
321D ALA 3.1 4.2 + - - -
323D LEU* 1.3 73.5 - - - +
325D ILE* 1.3 58.4 + - - +
327D TYR* 3.2 7.3 + - - +
328D ILE* 2.8 41.3 + - - +
336D HIS* 6.0 4.3 - - - -
497D LYS* 5.3 4.0 - - - -
501D GLN* 3.5 19.3 - - - -
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Residues in contact with ILE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 5.3 0.4 - - + -
10D PHE* 4.9 6.1 - - + -
13D LEU* 5.5 2.2 - - + -
68D LEU* 5.1 3.1 - - + -
71D LEU* 4.1 23.3 - - + -
321D ALA 3.0 17.3 + - - +
322D LEU* 3.4 11.2 - - + +
324D GLY* 1.3 74.6 - - - +
326D TRP* 1.3 58.4 + - - +
328D ILE* 4.5 0.9 - - - -
329D ASN* 2.8 47.2 + - + +
330D CYS* 3.7 1.1 + - - -
501D GLN* 4.0 15.0 - - + -
504D ILE* 4.1 29.6 - - + -
505D TRP* 3.5 38.1 - - + +
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Residues in contact with TRP 326 (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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13D LEU* 3.4 43.7 - - + -
16D TRP* 4.0 21.3 - + - -
17D TYR* 4.0 17.0 - + + -
24D LEU* 4.0 11.7 - - + -
59D LEU 2.8 29.1 + - - -
60D VAL* 3.8 13.6 - - + +
64D VAL* 3.9 21.3 - - + -
68D LEU* 4.3 10.7 - - + +
322D LEU 2.9 11.9 + - - +
323D LEU* 3.2 11.2 - - + +
324D GLY 3.2 0.2 - - - -
325D ILE* 1.3 77.0 - - - +
327D TYR* 1.3 76.2 + + - +
330D CYS* 3.1 45.2 + - + +
331D PHE* 3.2 27.8 + + - -
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Residues in contact with TYR 327 (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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58D ASN* 2.6 35.9 + - + +
59D LEU* 2.9 33.6 + - + -
323D LEU* 3.1 32.7 + - + +
324D GLY* 3.2 6.0 + - - +
326D TRP* 1.3 90.9 - + - +
328D ILE* 1.3 60.1 + - + +
331D PHE* 3.4 23.4 - + - +
332D GLY 2.9 9.9 + - - -
333D CYS* 2.8 27.3 + - + -
401D MET* 4.4 8.1 - - - -
403D PRO* 3.6 37.2 - - + -
473D PRO* 3.3 21.8 - - + +
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Residues in contact with ILE 328 (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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400C LYS* 4.5 4.5 - - - +
324D GLY* 2.8 30.3 + - - +
325D ILE 4.1 1.1 - - - +
327D TYR* 1.3 76.6 - - + +
329D ASN* 1.3 70.3 + - - +
332D GLY* 3.2 22.5 - - - -
333D CYS* 3.9 17.7 - - + +
335D THR 6.0 0.4 - - - +
374D GLN* 3.6 26.9 - - + +
375D THR 3.6 17.7 - - - +
377D PRO* 3.9 28.9 - - + -
501D GLN* 4.3 5.4 - - - +
505D TRP* 3.7 26.5 - - + -
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Residues in contact with ASN 329 (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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4D LEU* 4.0 6.7 - - - +
10D PHE* 3.7 29.7 - - + -
14D GLN* 5.0 5.2 + - - +
325D ILE* 2.8 29.9 + - + +
328D ILE* 1.3 76.1 - - - +
330D CYS* 1.3 62.9 + - - +
332D GLY* 4.6 0.4 - - - -
373D HIS* 3.9 10.5 + - + +
374D GLN* 2.9 42.6 + - - +
505D TRP* 2.7 26.6 + - - +
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Residues in contact with CYS 330 (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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10D PHE* 4.7 8.5 - - - -
13D LEU* 3.7 29.8 - - - -
14D GLN* 4.4 21.5 - - - -
17D TYR* 3.3 41.7 + - + -
325D ILE 3.7 1.1 + - - -
326D TRP* 3.1 30.3 + - + +
329D ASN* 1.3 82.1 - - - +
331D PHE* 1.3 61.6 + - - +
332D GLY* 3.2 2.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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