Contacts of the helix formed by residues 377 - 388 (chain B) in PDB entry 6MJL
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 GLY 377 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374B VAL 2.8 14.5 + - - -
375B ASN 3.0 3.8 + - - -
376B HIS* 1.3 77.2 - - - +
378B LEU* 1.3 59.8 + - - +
379B VAL 3.3 2.9 - - - -
380B PRO* 3.1 25.5 - - - +
381B PHE* 3.5 16.2 - - - -
415B TYR* 5.1 2.9 - - - -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 3.9 26.9 - - + +
340B PHE* 3.9 15.9 - - + -
341B PRO* 3.6 34.8 - - + -
344B LEU* 4.5 4.4 - - + +
359B MET* 3.7 33.7 - - + -
373B VAL* 3.2 22.2 + - + +
376B HIS* 3.8 19.1 - - + +
377B GLY* 1.3 76.8 - - - +
379B VAL* 1.3 60.0 + - - +
380B PRO 3.4 0.2 - - - -
381B PHE* 3.0 25.0 + - + +
382B LEU* 3.0 15.8 + - - +
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 4.4 8.1 - - + -
374B VAL* 4.1 12.8 - - + -
377B GLY 3.3 0.2 - - - -
378B LEU* 1.3 77.0 - - - +
380B PRO* 1.3 69.3 - - + +
382B LEU* 3.0 13.3 + - + +
383B VAL* 3.0 27.3 + - + +
401B ILE* 5.9 0.2 - - + -
404B TYR* 3.8 28.3 - - + +
415B TYR* 3.7 21.5 - - + -
416B LEU* 3.8 24.9 - - + -
419B CYS* 3.9 24.7 - - + -
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Residues in contact with PRO 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLY* 3.1 27.6 - - - +
379B VAL* 1.3 87.1 - - + +
381B PHE* 1.3 59.5 + - + +
383B VAL* 3.5 11.7 + - + +
384B GLY* 2.9 22.7 + - - -
415B TYR* 3.9 12.3 - - - +
419B CYS* 4.2 16.8 - - + +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B PRO* 3.5 51.8 - - + -
344B LEU* 3.8 20.4 - - + -
345B THR* 3.8 25.4 - - + -
376B HIS 5.5 0.7 - - - -
377B GLY 3.5 22.9 - - - -
378B LEU* 3.0 15.2 + - + +
380B PRO* 1.3 77.8 - - + +
382B LEU* 1.3 63.8 + - - +
384B GLY* 3.2 2.8 + - - +
385B VAL* 2.9 31.9 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.5 14.8 - - + -
356B THR* 4.5 14.4 - - + -
359B MET* 4.2 42.4 - - + -
363B THR* 4.7 8.7 - - + -
373B VAL* 4.9 3.6 - - + -
378B LEU 3.0 15.1 + - - +
379B VAL* 3.0 14.3 + - + +
381B PHE* 1.3 74.3 - - - +
383B VAL* 1.3 58.7 + - - +
385B VAL* 4.0 4.1 - - + +
386B LEU* 2.8 33.1 + - - +
397B ALA* 4.6 6.5 - - + +
400B ALA* 4.4 18.6 - - + -
401B ILE* 4.5 24.0 - - + +
404B TYR* 5.7 2.0 - - + -
421B ILE* 5.1 2.2 - - - -
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B VAL* 3.0 18.9 + - + +
380B PRO* 3.5 9.2 - - + +
382B LEU* 1.3 75.1 - - - +
384B GLY* 1.3 56.6 + - - +
386B LEU* 3.2 7.4 + - - +
387B SER* 2.7 37.5 + - - +
419B CYS* 3.9 32.3 - - + +
420B GLY* 3.6 22.0 - - - +
421B ILE* 4.1 23.1 - - + +
424B PRO* 4.1 8.3 - - + -
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B PRO 2.9 15.2 + - - -
381B PHE* 3.2 5.1 + - - -
382B LEU 3.2 0.4 - - - -
383B VAL* 1.3 75.3 - - - +
385B VAL* 1.3 57.0 + - - +
387B SER* 2.8 23.2 + - - -
388B LYS* 3.0 16.0 + - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B LEU* 3.2 33.9 - - + +
345B THR* 5.9 0.7 - - + -
352B GLN* 4.2 11.9 - - + +
356B THR* 3.9 14.1 - - + +
381B PHE 2.9 20.8 + - - +
382B LEU* 4.0 5.2 - - + +
384B GLY* 1.3 72.5 - - - +
386B LEU* 1.3 63.4 + - - +
387B SER 3.5 0.2 + - - -
388B LYS 3.7 7.5 + - - +
389B ALA* 3.2 17.8 - - + +
393B THR* 3.5 27.6 - - + +
394B GLN* 3.8 5.9 - - - +
397B ALA* 3.7 21.3 - - + -
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LEU 2.8 16.5 + - - +
383B VAL* 3.5 5.2 - - - +
385B VAL* 1.3 79.3 - - - +
387B SER* 1.3 57.6 + - - +
394B GLN* 2.9 32.3 + - - +
397B ALA* 3.5 22.7 - - + -
398B ALA* 3.9 11.9 - - + +
401B ILE* 4.5 7.2 - - + -
421B ILE* 3.5 28.9 - - + -
424B PRO* 4.0 10.2 - - + +
425B LEU* 3.5 31.0 - - + +
428B LEU* 3.8 29.0 - - + +
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL* 2.7 31.6 + - - +
384B GLY* 2.8 9.3 + - - -
386B LEU* 1.3 75.4 - - - +
388B LYS* 1.3 61.0 + - - +
394B GLN* 4.1 5.1 + - - -
424B PRO* 3.5 21.8 - - - +
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B GLN* 4.6 3.1 - - - +
384B GLY 3.0 13.2 + - - +
385B VAL* 3.8 2.9 - - - +
386B LEU 3.5 0.6 - - - -
387B SER* 1.3 83.3 - - - +
389B ALA* 1.3 69.1 + - - +
394B GLN* 4.5 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
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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