Contacts of the helix formed by residues 314 - 329 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.1 1.3 - - - -
80C ARG* 4.1 3.8 - - - +
305C HIS* 3.7 6.2 + - - -
306C PHE* 2.8 45.4 + - - +
309C THR* 2.9 21.2 + - - +
310C PRO 3.1 11.6 + - - +
311C LEU* 3.2 11.6 + - - +
312C GLU 3.6 0.4 - - - -
313C LYS* 1.3 75.5 - - - +
315C ALA* 1.3 65.9 + - - +
316C PRO* 3.0 29.7 - - - +
317C VAL* 3.2 19.2 + - + +
318C LEU* 2.9 23.2 + - - +
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.8 15.5 - - + -
43C LEU* 4.1 15.7 - - + -
52C VAL* 4.5 11.6 - - + +
302C MET* 5.2 0.7 - - - -
305C HIS* 3.0 20.9 - - + -
313C LYS 3.5 3.0 + - - -
314C ASN* 1.3 71.3 - - - +
316C PRO* 1.3 68.7 - - + +
317C VAL 3.2 0.2 + - - -
318C LEU* 3.3 2.9 + - - +
319C LEU* 3.0 29.5 + - - +
492C MET* 4.3 17.3 - - - -
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Residues in contact with PRO 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C MET* 4.2 8.7 - - - -
305C HIS* 3.8 8.3 - - - +
306C PHE* 3.9 22.7 - - + -
314C ASN* 3.0 20.6 - - - +
315C ALA* 1.3 88.8 - - + +
317C VAL* 1.3 60.5 + - - +
319C LEU* 3.4 2.6 + - + +
320C ALA* 3.0 23.0 + - - +
492C MET* 3.7 29.4 - - + +
495C HIS* 3.7 26.2 - - + +
496C LYS* 3.5 12.6 - - + +
499C VAL* 4.7 0.9 - - - -
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ALA* 4.6 6.3 - - + -
76C VAL* 4.7 2.7 - - + -
306C PHE* 3.7 19.3 - - + -
311C LEU* 4.0 35.4 - - + +
314C ASN* 3.2 33.4 + - + +
315C ALA 3.2 0.4 - - - -
316C PRO* 1.3 74.9 - - - +
318C LEU* 1.3 66.9 - - - +
320C ALA* 3.0 2.4 + - - +
321C LEU* 2.8 51.9 + - + +
499C VAL* 4.1 14.8 - - + -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 3.8 16.8 - - + -
52C VAL* 6.2 1.6 - - + -
54C TYR* 3.6 42.8 - - + +
64C MET* 4.0 19.7 - - + +
68C VAL* 4.7 4.5 - - + -
311C LEU 3.6 18.2 - - - +
312C GLU* 3.6 23.1 - - - +
314C ASN 2.9 19.5 + - - +
315C ALA* 3.8 4.0 - - - +
317C VAL* 1.3 74.6 - - - +
319C LEU* 1.3 59.3 + - + +
321C LEU* 3.7 15.4 - - + +
322C LEU* 2.9 38.1 + - + +
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 4.2 20.4 - - + -
54C TYR* 6.2 0.4 - - + -
315C ALA 3.0 20.7 + - - +
316C PRO* 3.7 5.4 - - + +
318C LEU* 1.3 77.1 - - + +
320C ALA* 1.3 62.9 + - - +
322C LEU* 3.6 9.1 + - + +
323C GLY 3.1 15.6 + - - -
404C ASP* 5.1 3.4 - - - +
474C ASN* 3.7 31.5 + - - +
476C ILE* 4.4 11.7 - - + -
492C MET* 3.8 39.3 - - + -
493C TYR* 4.7 12.8 - - + -
496C LYS* 3.6 25.4 - - + +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C PRO 3.0 11.7 + - - +
317C VAL 3.0 9.1 + - - +
319C LEU* 1.3 76.8 - - - +
321C LEU* 1.3 57.7 + - - +
323C GLY 2.9 4.2 + - - -
324C ILE* 2.9 27.7 + - - +
496C LYS* 3.5 31.6 - - - +
499C VAL* 3.5 23.1 - - + -
500C GLN* 3.2 17.9 + - + +
503C ILE* 5.3 0.4 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 5.4 2.2 - - + -
67C LEU* 3.8 53.9 - - + +
68C VAL* 3.8 17.9 - - + +
70C LEU* 6.4 0.4 - - + -
71C ALA* 4.4 4.7 - - + -
317C VAL* 2.8 51.8 + - + +
318C LEU* 3.7 13.5 - - + +
320C ALA* 1.3 76.0 - - + +
322C LEU* 1.3 65.5 + - + +
324C ILE* 3.0 10.0 + - - +
325C TRP* 2.9 23.2 + - - +
499C VAL* 4.2 2.5 - - + -
503C ILE* 4.1 22.0 - - + -
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.5 35.4 - - + -
57C ASN* 3.8 22.7 - - + +
59C VAL* 4.6 5.6 - - + -
64C MET* 4.1 28.0 - - + -
67C LEU* 4.7 3.4 - - + -
318C LEU* 2.9 27.6 + - + +
319C LEU* 3.8 9.4 - - + +
321C LEU* 1.3 74.4 - - - +
323C GLY* 1.3 61.3 + - - +
325C TRP* 3.3 8.9 - - + +
326C TYR* 3.1 40.3 + - + +
474C ASN* 3.7 20.4 - - - +
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Residues in contact with GLY 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU 3.1 9.2 + - - -
320C ALA 2.9 9.5 + - - -
322C LEU* 1.3 75.6 - - - +
324C ILE* 1.3 58.3 + - - +
326C TYR* 3.4 5.4 + - - +
327C ILE* 2.9 40.4 + - - +
335C HIS* 6.0 3.8 - - - -
402C PRO* 6.5 0.4 - - - -
496C LYS* 5.2 3.6 - - - -
500C GLN* 3.6 16.4 - - - -
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Residues in contact with ILE 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 5.8 0.7 - - + -
9C PHE* 5.0 5.6 - - + -
12C LEU* 5.6 1.3 - - + -
67C LEU* 5.0 4.7 - - + -
70C LEU* 4.2 23.3 - - + -
320C ALA 2.9 18.0 + - - +
321C LEU* 3.0 8.7 + - - +
323C GLY* 1.3 74.4 - - - +
325C TRP* 1.3 60.0 + - - +
327C ILE* 4.6 0.9 - - - -
328C ASN* 2.8 46.2 + - + +
329C CYS* 3.8 2.4 + - - +
500C GLN* 4.3 13.7 - - + -
503C ILE* 4.0 34.1 - - + -
504C TRP* 3.5 37.9 - - + +
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Residues in contact with TRP 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.6 32.8 - - + -
15C TRP* 3.9 32.8 - + - -
16C TYR* 4.0 15.9 - + + -
23C LEU* 4.3 4.7 - - + -
58C LEU 2.9 23.9 + - - -
59C VAL* 5.0 3.8 - - + -
63C VAL* 3.8 24.8 - - + +
67C LEU* 4.2 15.5 - - + +
321C LEU 2.9 11.5 + - - +
322C LEU* 3.3 13.0 - - + +
324C ILE* 1.3 77.2 - - - +
326C TYR* 1.3 80.4 + + - +
329C CYS* 3.0 60.4 + - - +
330C PHE* 3.2 22.3 + + - -
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Residues in contact with TYR 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ASN* 2.6 35.7 + - + +
58C LEU* 2.9 31.1 + - + -
322C LEU* 3.1 32.2 + - + +
323C GLY* 4.1 4.5 - - - +
325C TRP* 1.3 93.7 - + - +
327C ILE* 1.3 60.0 + - + +
330C PHE* 3.2 13.4 - + - +
331C GLY 3.0 9.0 + - - -
332C CYS* 2.9 24.8 + - + +
400C MET* 3.3 32.3 - - + -
402C PRO* 3.7 34.8 - - + -
472C PRO* 3.2 13.0 - - + +
474C ASN* 6.1 0.9 - - - -
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C GLY* 2.9 26.7 + - - +
324C ILE* 4.1 1.6 - - - +
326C TYR* 1.3 80.8 - - + +
328C ASN* 1.3 71.3 + - - +
331C GLY* 3.3 21.7 - - - -
332C CYS* 3.8 20.6 - - + +
334C THR 5.8 1.3 - - - +
335C HIS* 6.2 0.4 - - + -
373C GLN* 3.9 24.1 - - + +
374C THR 3.8 14.8 - - - +
376C PRO* 3.7 39.5 - - + -
402C PRO* 6.4 0.2 - - + -
500C GLN* 4.6 4.0 - - - +
504C TRP* 4.0 15.5 - - + -
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Residues in contact with ASN 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 5.1 2.1 - - - +
9C PHE* 3.8 25.9 - - + -
13C GLN* 3.0 23.6 + - - -
324C ILE* 2.8 30.4 + - + +
327C ILE* 1.3 78.3 - - - +
329C CYS* 1.3 61.2 + - - +
331C GLY* 4.6 0.9 - - - -
372C HIS* 4.0 9.8 + - + +
373C GLN* 3.0 39.4 + - - +
504C TRP* 2.8 27.1 + - - +
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Residues in contact with CYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 5.1 7.0 - - - -
12C LEU* 4.6 6.5 - - - -
13C GLN* 4.4 30.5 - - - +
16C TYR* 3.2 40.9 + - + -
324C ILE* 3.8 2.0 + - - -
325C TRP* 3.0 46.6 + - + +
328C ASN* 1.3 83.8 - - - +
330C PHE* 1.3 61.4 + - - +
331C GLY 3.2 1.9 + - - -
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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
------------------------------------------------------------
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