Contacts of the helix formed by residues 348 - 359 (chain B) in PDB entry 2DH3
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 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B GLY* 5.1 11.9 - - - +
344B LEU* 4.6 13.7 - - + -
345B PRO* 3.3 32.8 + - + +
346B ALA 3.2 0.8 - - - -
347B GLN* 1.3 87.4 - - - +
349B LEU* 1.3 60.4 + - - +
350B ARG 3.4 2.7 - - - -
351B LEU* 3.3 25.4 + - + +
352B TYR* 3.0 47.5 + - + -
468B PHE* 4.8 7.4 - - + -
518B HIS* 3.7 28.0 - - + +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 4.2 23.6 - - + +
341B THR* 4.0 26.2 - - + -
344B LEU* 4.0 31.6 - - + +
345B PRO 3.7 5.4 - - - +
346B ALA* 3.3 32.7 + - + +
347B GLN 3.6 0.2 - - - -
348B LEU* 1.3 78.6 - - - +
350B ARG* 1.3 62.3 + - + +
352B TYR* 4.2 4.1 - - - +
353B GLN* 3.2 30.1 + - - +
372B GLY* 4.6 6.5 - - - +
418B LEU* 4.4 26.0 - - + -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLN* 5.4 2.4 - - - +
348B LEU 3.4 0.4 - - - -
349B LEU* 1.3 75.1 - - + +
351B LEU* 1.3 66.2 + - - +
353B GLN* 3.3 3.0 + - - +
354B LEU* 3.1 23.2 + - - +
416B GLY* 2.9 28.2 + - - -
417B SER* 3.9 11.7 + - - +
418B LEU* 3.4 31.8 - - + +
421B LEU* 3.8 28.7 - - + +
498B THR* 3.5 42.9 + - - +
499B GLN* 5.9 2.0 - - - -
500B PRO* 5.6 2.4 - - - +
518B HIS 6.0 0.4 - - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLN 5.5 0.6 + - - +
348B LEU* 3.3 24.8 + - + +
350B ARG* 1.3 80.5 - - - +
352B TYR* 1.3 61.6 + - + +
354B LEU* 3.5 4.5 + - - +
355B MET* 3.2 21.7 + - - +
466B LEU* 3.9 14.4 - - + +
467B ASN 3.4 23.8 - - - +
468B PHE* 3.7 35.7 - - + -
498B THR* 4.2 4.6 - - + +
518B HIS 3.5 15.4 + - - +
519B GLU 3.4 36.1 - - - +
520B GLY* 3.4 11.2 - - - +
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Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.3 11.3 + - + -
307B SER 3.9 5.0 + - - -
308B GLY* 3.1 29.0 + - - -
314B THR* 4.9 3.3 + - + +
334B LEU* 4.4 24.7 - - + -
340B LEU* 5.6 3.8 - - + -
344B LEU* 3.4 44.7 - - + +
348B LEU* 3.0 36.4 + - + +
349B LEU 4.4 2.7 - - - +
351B LEU* 1.3 77.7 - - + +
353B GLN* 1.3 58.9 + - - +
355B MET* 3.5 29.1 + - + +
356B LEU* 3.1 37.6 + - + +
468B PHE* 3.7 27.9 - + - -
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Residues in contact with GLN 353 (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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340B LEU* 4.4 18.2 - - + +
349B LEU* 3.2 22.4 + - - +
350B ARG* 3.6 5.6 - - - +
351B LEU 3.3 0.4 - - - -
352B TYR* 1.3 74.6 - - - +
354B LEU* 1.3 64.3 + - - +
356B LEU* 3.5 5.6 + - - +
357B PHE* 3.2 31.4 + - + -
365B PHE* 4.6 9.1 - - + -
369B ASP* 2.9 30.9 + - - +
370B GLU* 4.3 0.8 - - - +
418B LEU* 3.9 33.6 - - - +
421B LEU* 4.3 3.9 - - + +
422B PHE* 3.8 31.2 + - + +
425B LEU* 3.9 8.0 - - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG 3.1 12.9 + - - +
351B LEU 3.7 7.6 - - - +
353B GLN* 1.3 75.8 - - - +
355B MET* 1.3 55.1 + - - +
357B PHE* 3.4 2.3 + - - +
358B THR* 2.7 50.5 + - + +
421B LEU* 5.8 0.4 - - + -
425B LEU* 3.5 33.3 - - + +
464B VAL* 4.5 6.5 - - + -
466B LEU* 3.7 17.5 - - + -
496B LEU* 4.7 4.9 - - + -
498B THR* 4.5 6.5 - - + -
520B GLY* 3.7 34.1 - - - +
521B LEU 4.0 11.4 - - - +
522B LEU* 4.2 17.9 - - + +
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Residues in contact with MET 355 (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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304B LEU* 4.0 28.3 - - + -
314B THR* 4.2 12.1 - - + -
318B VAL* 5.3 1.8 - - + -
351B LEU 3.2 11.7 + - - +
352B TYR* 3.7 32.1 - - + +
353B GLN 3.3 0.2 - - - -
354B LEU* 1.3 80.7 - - - +
356B LEU* 1.3 63.2 + - + +
358B THR* 3.1 8.8 + - - -
359B LEU* 3.1 48.5 + - + +
450B PHE* 4.2 15.0 - - + -
452B TYR* 3.8 7.6 - - - +
466B LEU* 3.9 18.6 - - + +
468B PHE* 4.0 23.6 - - - -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 4.4 12.8 - - + -
332B TRP* 3.7 42.9 - - + +
333B SER* 4.2 4.9 - - - +
334B LEU* 3.8 29.6 - - + -
340B LEU* 4.4 7.9 - - + -
352B TYR 3.1 21.0 + - - +
353B GLN* 4.0 4.3 - - - +
354B LEU 3.4 0.2 - - - -
355B MET* 1.3 86.6 - - + +
357B PHE* 1.3 60.1 + - - +
358B THR 3.6 0.2 + - - -
359B LEU* 4.2 10.3 + - + +
361B GLY 5.2 0.5 - - - +
363B PRO* 3.4 23.2 - - + +
364B VAL 5.5 1.1 - - - +
365B PHE* 3.9 32.5 - - + -
429B ARG* 5.7 0.2 + - - -
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Residues in contact with PHE 357 (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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122B ALA* 4.3 16.2 - - + -
353B GLN* 3.2 26.5 + - + +
354B LEU 4.0 3.4 - - - +
355B MET 3.3 0.2 - - - -
356B LEU* 1.3 75.7 - - - +
358B THR* 1.3 62.5 + - + +
359B LEU 3.7 1.1 - - - -
363B PRO* 4.4 6.1 - - + -
365B PHE* 3.8 17.0 - + - -
422B PHE* 3.8 45.3 - + - -
425B LEU* 3.6 38.8 - - + +
426B SER* 3.6 28.9 - - - -
429B ARG* 3.4 51.0 - - + +
435B LEU* 5.0 4.0 - - - +
454B ARG* 5.5 0.2 + - - -
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Residues in contact with THR 358 (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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354B LEU* 2.7 40.5 + - + +
355B MET* 3.1 0.9 + - - -
357B PHE* 1.3 85.4 - - + +
359B LEU* 1.3 58.4 + - - +
425B LEU* 5.3 1.6 - - + -
435B LEU* 4.5 19.0 - - + +
452B TYR* 2.5 36.3 + - - -
454B ARG* 2.8 25.8 + - - +
464B VAL* 4.0 19.0 - - + +
522B LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 5.1 0.7 - - + -
318B VAL* 4.2 21.1 - - + -
332B TRP* 3.4 53.3 - - + +
355B MET* 3.1 38.2 + - + +
356B LEU* 4.2 6.2 + - + +
357B PHE 3.7 0.6 - - - -
358B THR* 1.3 78.8 - - - +
360B PRO* 1.3 66.3 - - + +
361B GLY 3.0 17.2 + - - +
429B ARG* 4.9 3.6 + - - -
440B PHE* 3.8 28.0 - - + -
450B PHE* 5.1 1.1 - - + -
452B TYR* 4.0 16.6 - - + -
454B ARG* 3.3 7.4 + - - -
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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