Contacts of the helix formed by residues 376 - 384 (chain C) in PDB entry 5M8L
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 LEU 376 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 4.3 13.5 - - + -
328C PRO* 3.8 13.3 - - + +
332C ASP* 3.8 42.2 - - + +
333C VAL* 4.2 16.4 - - + -
336C CYS* 4.3 11.2 - - + -
358C THR* 3.5 24.9 - - + +
359C VAL* 3.6 22.0 - - + +
361C GLY* 3.7 3.2 - - - -
365C PRO* 4.7 4.5 - - + -
375C SER* 1.3 91.2 + - - +
377C HIS* 1.3 71.1 + - - +
378C ASN 3.1 0.4 - - - -
379C LEU* 2.7 13.2 + - - +
380C ALA* 3.0 14.0 + - - +
410C VAL* 6.4 1.1 - - + -
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Residues in contact with HIS 377 (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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215C HIS* 4.8 7.2 - + - -
220C PHE* 3.5 26.1 - + + -
251C PHE* 4.4 13.2 - - + -
359C VAL 3.2 13.2 + - - +
360C GLU* 3.1 14.5 + - + +
376C LEU* 1.3 79.8 - - - +
378C ASN* 1.3 79.9 + - - +
380C ALA* 3.6 2.9 + - - +
381C HIS* 3.1 37.2 + + - -
403C LEU* 3.7 17.0 - - + +
404C HIS* 2.9 17.6 - + - -
407C THR* 3.9 12.1 - - + +
513C ZN 1.8 38.7 - - - -
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Residues in contact with ASN 378 (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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360C GLU* 2.9 24.8 + - - +
361C GLY 3.3 23.7 + - - +
362C TYR* 3.2 41.1 + - - -
374C ARG* 4.1 13.0 - - - +
376C LEU 3.1 0.8 - - - -
377C HIS* 1.3 95.1 + - - +
379C LEU* 1.3 65.2 + - - +
381C HIS* 3.2 7.7 + - - +
382C LEU* 3.0 31.9 + - + +
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Residues in contact with LEU 379 (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 MET 3.3 26.2 - - - +
324C VAL* 3.7 16.4 - - + -
326C ARG 3.3 25.6 - - - +
327C LEU* 3.9 2.0 - - - -
328C PRO* 3.5 22.2 - - + -
332C ASP* 5.5 0.7 - - - +
374C ARG* 3.7 19.3 - - + +
375C SER* 3.5 26.5 - - - +
376C LEU 2.7 16.3 + - - +
378C ASN* 1.3 73.1 - - - +
380C ALA* 1.3 52.9 + - - +
382C LEU* 3.0 3.0 + - - +
383C PHE* 2.6 36.3 + - - +
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Residues in contact with ALA 380 (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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249C TRP* 4.6 2.8 - - + -
251C PHE* 3.9 33.2 - - + -
327C LEU* 4.0 15.7 - - + -
328C PRO* 4.7 1.2 - - + +
376C LEU 3.0 9.0 + - - +
377C HIS 3.9 5.2 - - - +
379C LEU* 1.3 76.8 - - - +
381C HIS* 1.3 62.2 + - - +
383C PHE* 3.5 5.9 + - - +
384C LEU* 3.4 23.2 + - - +
403C LEU* 3.7 22.3 - - + +
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Residues in contact with HIS 381 (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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377C HIS* 3.1 32.2 + + - +
378C ASN* 3.2 12.2 + - - +
379C LEU 3.1 0.6 - - - -
380C ALA* 1.3 81.0 - - - +
382C LEU* 1.3 62.3 + - + +
384C LEU* 3.5 10.3 + - - +
385C ASN 4.2 1.0 + - - -
388C GLY 2.5 31.6 + - - +
389C GLY* 3.3 24.8 + - - -
394C SER* 3.7 22.2 - - - -
400C PHE* 3.8 12.1 - + + -
403C LEU* 3.7 20.9 - - + +
404C HIS* 3.6 3.2 + - - -
513C ZN 2.3 35.4 - - - -
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Residues in contact with LEU 382 (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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318C ASN* 5.1 2.6 + - - +
321C ARG* 3.8 24.2 - - - +
324C VAL* 3.6 36.9 - - + +
374C ARG* 3.6 38.1 - - + +
378C ASN* 3.0 24.1 + - + +
379C LEU* 3.8 1.3 - - - +
381C HIS* 1.3 74.3 - - + +
383C PHE* 1.3 64.3 + - - +
384C LEU 3.2 0.7 - - - -
385C ASN* 3.1 17.0 + - - +
389C GLY* 4.4 17.9 - - - +
511C NAG 5.4 2.4 - - - +
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Residues in contact with PHE 383 (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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249C TRP* 4.8 0.9 - + - -
255C LYS 4.1 0.9 - - - -
256C ASN 3.5 20.0 - - - -
257C VAL 3.9 12.8 - - - -
258C CYS* 4.1 12.6 - - + -
315C PRO* 3.7 17.7 - - + -
316C ALA* 3.0 54.3 + - + -
324C VAL* 3.3 11.4 + - - +
325C GLN 3.8 9.4 - - - -
326C ARG* 3.7 25.1 - - - +
327C LEU* 3.4 37.9 - - + -
379C LEU 2.6 21.4 + - - +
380C ALA 3.6 4.9 - - - +
381C HIS 3.3 0.2 - - - -
382C LEU* 1.3 73.1 - - - +
384C LEU* 1.3 72.1 + - + +
385C ASN* 3.1 2.9 + - - +
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Residues in contact with LEU 384 (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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249C TRP* 4.5 10.3 - - + -
258C CYS* 5.0 2.2 - - - -
313C ARG* 3.8 17.0 - - + +
314C ASN 2.9 26.8 + - - -
315C PRO* 4.2 8.1 - - + -
380C ALA 3.4 16.2 - - - +
381C HIS* 3.5 11.4 + - + +
382C LEU 3.2 1.2 - - - -
383C PHE* 1.3 92.6 - - + +
385C ASN* 1.3 66.1 + - - +
386C GLY 3.2 4.1 + - - +
388C GLY* 4.4 19.3 - - - +
397C ASP* 4.3 13.2 - - - +
399C ILE* 4.2 37.0 - - + -
400C PHE 5.8 0.9 - - - +
403C LEU* 4.8 6.1 - - + -
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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
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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