Contacts of the helix formed by residues 314 - 329 (chain D) in PDB entry 1JLH
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 314 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU* 4.3 0.2 - - - -
80D ARG* 4.2 3.4 - - - +
305D HIS* 3.7 3.3 + - - -
306D PHE* 2.8 41.7 + - - +
309D THR* 3.1 23.6 + - - +
310D PRO 3.0 11.1 + - - +
311D LEU* 3.1 11.7 + - - +
313D LYS* 1.3 74.1 - - - +
315D ALA* 1.3 58.5 + - - +
316D PRO* 3.0 26.7 - - - +
317D VAL* 3.2 22.8 + - + +
318D LEU* 2.9 31.5 + - - +
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.7 20.2 - - + -
43D LEU* 4.3 11.2 - - + -
52D VAL* 4.4 8.9 - - + +
302D MET* 5.2 0.4 - - - -
305D HIS* 3.1 20.4 - - + -
313D LYS 3.5 3.2 + - - -
314D ASN* 1.3 69.5 - - - +
316D PRO* 1.3 73.0 - - + +
317D VAL 3.2 0.2 + - - -
318D LEU* 3.2 2.2 + - - +
319D LEU* 3.0 29.5 + - - +
492D MET* 4.2 19.3 - - + -
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Residues in contact with PRO 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D MET* 4.3 8.5 - - + -
305D HIS* 3.9 8.7 - - - +
306D PHE* 4.3 12.3 - - + -
314D ASN* 3.0 21.3 - - - +
315D ALA* 1.3 87.8 - - + +
317D VAL* 1.3 55.4 + - - +
319D LEU* 3.5 1.7 + - + +
320D ALA* 3.0 29.8 + - - +
492D MET* 3.6 41.5 - - + +
495D HIS* 3.7 22.7 - - + -
496D LYS* 3.5 12.4 - - + +
499D VAL* 4.7 0.9 - - - -
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA* 4.6 5.2 - - + -
76D VAL* 4.6 2.9 - - + -
80D ARG* 5.8 0.2 - - - +
306D PHE* 3.9 19.3 - - + -
311D LEU* 4.0 37.5 - - + +
314D ASN* 3.2 30.9 + - + +
315D ALA 3.1 0.4 - - - -
316D PRO* 1.3 75.1 - - - +
318D LEU* 1.3 61.1 + - - +
320D ALA* 3.2 3.2 + - - +
321D LEU* 2.8 50.5 + - + +
499D VAL* 4.0 16.8 - - + -
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Residues in contact with LEU 318 (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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41D LEU* 3.9 18.2 - - + -
52D VAL* 6.4 0.9 - - + -
54D TYR* 3.7 35.9 - - + +
64D MET* 4.0 22.7 - - + -
68D VAL* 4.7 3.8 - - + -
311D LEU 3.6 16.4 - - - +
312D GLU* 3.4 27.1 - - - +
313D LYS* 4.4 0.2 - - - -
314D ASN 2.9 18.1 + - - +
315D ALA* 3.9 3.8 - - - +
317D VAL* 1.3 73.2 - - - +
319D LEU* 1.3 61.6 + - + +
321D LEU* 3.1 17.5 + - + +
322D LEU* 2.8 40.7 + - + +
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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
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52D VAL* 4.3 20.9 - - + -
54D TYR* 5.7 0.9 - - + -
315D ALA 3.0 19.5 + - - +
316D PRO* 3.8 5.2 - - + +
318D LEU* 1.3 75.7 - - + +
320D ALA* 1.3 63.3 + - - +
322D LEU* 3.5 9.4 + - + +
323D GLY* 3.2 16.6 + - - -
404D ASP* 5.0 5.6 - - - +
474D ASN* 3.7 31.7 + - + +
476D ILE* 4.7 5.4 - - + -
492D MET* 3.8 41.1 - - + -
493D TYR* 4.7 16.6 - - + +
496D LYS* 3.8 24.4 - - + +
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Residues in contact with ALA 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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316D PRO 3.0 18.4 + - - +
317D VAL 3.4 4.9 - - - +
318D LEU 3.2 0.2 - - - -
319D LEU* 1.3 77.2 - - - +
321D LEU* 1.3 57.2 + - - +
323D GLY 3.1 2.4 + - - -
324D ILE* 3.0 28.6 + - - +
496D LYS* 3.5 31.8 - - + +
499D VAL* 3.5 18.6 - - + -
500D GLN* 3.1 18.6 + - + +
503D ILE* 5.5 0.2 - - + -
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Residues in contact with LEU 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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64D MET* 5.4 1.6 - - + -
67D LEU* 3.6 56.7 - - + +
68D VAL* 3.8 11.4 - - + +
70D LEU* 5.7 1.8 - - + -
71D ALA* 4.2 9.6 - - + -
317D VAL* 2.8 38.6 + - + +
318D LEU* 3.1 19.9 + - + +
320D ALA* 1.3 72.5 - - - +
322D LEU* 1.3 66.2 + - - +
324D ILE* 3.2 6.5 + - + +
325D TRP* 3.0 22.9 + - - +
499D VAL* 4.6 2.5 - - + -
503D ILE* 3.6 28.3 - - + -
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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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54D TYR* 3.5 35.7 - - + -
57D ASN* 3.7 15.7 - - + +
59D VAL* 3.8 29.4 - - + -
64D MET* 4.2 18.2 - - + -
67D LEU* 4.8 2.0 - - + -
318D LEU* 2.8 28.1 + - + +
319D LEU* 3.8 8.7 - - + +
321D LEU* 1.3 72.7 - - - +
323D GLY* 1.3 61.9 + - - +
325D TRP* 3.2 7.5 - - + +
326D TYR* 3.1 39.0 + - + -
474D ASN* 3.5 21.1 - - - +
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Residues in contact with GLY 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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319D LEU 3.2 8.9 + - - -
320D ALA 3.1 7.7 + - - -
321D LEU 3.1 0.8 - - - -
322D LEU* 1.3 74.9 - - - +
324D ILE* 1.3 59.0 + - - +
326D TYR* 3.4 5.9 + - - +
327D ILE* 2.9 39.1 + - - +
335D HIS* 6.0 4.5 - - - -
496D LYS* 5.3 3.1 - - - -
500D GLN* 3.5 15.9 - - - -
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Residues in contact with ILE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 5.3 1.3 - - + -
9D PHE* 5.0 5.6 - - + -
12D LEU* 5.9 1.3 - - + -
67D LEU* 5.3 4.0 - - + -
70D LEU* 4.4 21.3 - - + -
320D ALA 3.0 19.4 + - - +
321D LEU* 3.2 8.3 + - + +
323D GLY* 1.3 75.9 - - - +
325D TRP* 1.3 58.6 + - - +
327D ILE* 4.5 2.0 - - - -
328D ASN* 2.7 50.3 + - + +
329D CYS* 3.8 1.0 + - - -
500D GLN* 4.2 13.2 - - + -
503D ILE* 4.1 31.4 - - + -
504D TRP* 3.4 40.2 - - + +
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Residues in contact with TRP 325 (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 LEU* 3.8 31.2 - - + -
15D TRP* 4.0 17.0 - + - -
16D TYR* 3.9 20.4 - + + -
23D LEU* 4.2 16.6 - - + -
58D LEU 3.0 20.1 + - - -
59D VAL* 3.9 17.4 - - + +
63D VAL* 3.8 17.9 - - + -
67D LEU* 4.2 13.2 - - + +
321D LEU 3.0 12.5 + - - +
322D LEU* 3.2 12.1 - - + +
324D ILE* 1.3 77.9 - - - +
326D TYR* 1.3 76.1 + + - +
329D CYS* 3.0 62.8 + - + +
330D PHE* 3.2 23.7 + + - -
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Residues in contact with TYR 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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57D ASN* 2.7 31.1 + - + +
58D LEU* 3.0 28.3 + - + -
322D LEU* 3.1 30.9 + - + +
323D GLY* 4.0 4.9 - - - +
325D TRP* 1.3 91.8 - + - +
327D ILE* 1.3 60.6 + - + +
330D PHE* 3.1 16.5 - + - +
331D GLY 2.9 23.9 + - - -
332D CYS* 2.9 12.7 + - + -
400D MET* 3.7 31.9 - - + -
402D PRO* 3.7 37.7 - - + -
472D PRO* 3.0 13.4 - - + +
474D ASN* 6.1 1.3 - - - -
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Residues in contact with ILE 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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323D GLY* 2.9 25.1 + - - +
324D ILE* 4.0 1.8 - - - +
326D TYR* 1.3 79.5 - - + +
328D ASN* 1.3 67.4 + - - +
331D GLY* 3.2 22.9 - - - -
332D CYS* 3.7 21.5 - - + +
334D THR 5.8 1.1 - - - +
335D HIS* 6.2 0.7 - - + -
373D GLN* 3.9 24.5 - - + +
374D THR 3.7 15.7 - - - +
376D PRO* 3.6 42.0 - - + -
402D PRO* 6.5 0.2 - - + -
500D GLN* 4.6 4.7 - - - +
504D TRP* 3.9 15.5 - - + -
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Residues in contact with ASN 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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3D LEU* 4.0 7.6 - - - +
9D PHE* 3.9 28.7 - - + -
13D GLN* 4.7 5.9 + - - -
324D ILE* 2.7 35.1 + - + +
327D ILE* 1.3 77.1 - - - +
329D CYS* 1.3 60.5 + - - +
331D GLY* 4.6 0.7 - - - -
372D HIS* 4.1 9.3 + - - +
373D GLN* 2.9 38.6 + - - +
504D TRP* 2.7 25.5 + - - +
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Residues in contact with CYS 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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9D PHE* 4.5 13.0 - - - -
12D LEU* 4.6 4.7 - - - -
13D GLN* 4.5 24.9 - - - -
16D TYR* 3.1 37.3 + - + -
324D ILE* 5.1 0.7 - - - -
325D TRP* 3.0 53.0 + - + +
328D ASN* 1.3 84.2 - - - +
330D PHE* 1.3 60.9 + - - +
331D GLY 3.3 1.1 - - - -
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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