Contacts of the helix formed by residues 417 - 432 (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 SER 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B ARG* 3.9 4.6 + - - +
411B GLN* 2.7 45.4 + - - +
414B ASP* 3.1 27.2 + - - -
415B PRO 3.3 0.9 - - - +
416B GLY* 1.3 82.6 - - - +
418B LEU* 1.3 63.2 + - - +
419B LEU 3.5 2.1 + - - -
420B SER* 3.1 14.2 + - - -
421B LEU* 3.3 20.1 + - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B LEU* 4.4 15.9 - - + -
350B ARG* 3.4 50.1 - - + +
353B GLN* 3.9 25.6 - - - +
370B GLU 3.3 12.1 - - - +
371B ILE 3.9 2.7 - - - +
372B GLY* 3.5 35.0 - - - +
411B GLN* 3.5 9.8 + - - +
417B SER* 1.3 72.9 - - - +
419B LEU* 1.3 60.0 + - - +
421B LEU* 3.5 7.8 + - + +
422B PHE* 3.0 23.9 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 4.3 2.0 - - - +
153B LEU* 3.7 31.6 - - + -
370B GLU* 3.2 28.0 + - + +
371B ILE* 4.3 7.2 - - + -
408B VAL* 4.1 19.3 - - + +
411B GLN* 3.1 28.3 + - + +
412B SER* 3.5 26.2 - - - +
417B SER* 3.3 0.6 - - - +
418B LEU* 1.3 76.3 - - - +
420B SER* 1.3 58.8 + - - +
422B PHE* 3.5 2.0 - - + +
423B ARG* 2.9 47.8 + - + +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLN 3.7 4.5 + - - -
412B SER* 5.3 1.9 - - - -
414B ASP 2.7 23.6 + - - -
415B PRO* 3.3 26.0 + - - +
417B SER* 3.1 9.2 + - - -
419B LEU* 1.3 75.1 - - - +
421B LEU* 1.3 61.9 + - - +
423B ARG* 3.4 8.7 + - - +
424B ARG* 2.9 37.5 + - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG* 3.8 52.3 - - + +
353B GLN* 4.3 10.5 - - - +
354B LEU* 5.8 0.2 - - + -
415B PRO 5.0 0.4 + - - -
417B SER 3.3 11.1 + - - +
418B LEU* 3.6 9.0 - - + +
420B SER* 1.3 79.9 - - - +
422B PHE* 1.3 60.4 + - - +
424B ARG* 3.4 6.4 + - - +
425B LEU* 3.0 41.4 + - + +
496B LEU* 3.9 32.3 - - + -
497B SER 3.9 13.7 - - - +
498B THR* 4.3 8.1 - - + +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 5.2 4.0 - - + -
124B TYR* 5.6 4.0 - + - -
153B LEU* 4.1 39.0 - - + -
155B VAL* 5.2 6.5 - - + -
353B GLN* 3.8 21.5 + - - +
357B PHE* 3.8 34.6 - + - -
365B PHE* 3.9 33.4 - + + -
369B ASP* 5.3 0.2 - - + -
370B GLU* 3.8 34.5 - - + -
418B LEU 3.0 18.3 + - - +
419B LEU* 3.5 9.4 - - - +
421B LEU* 1.3 76.8 - - - +
423B ARG* 1.3 59.5 + - - +
425B LEU* 3.4 1.8 + - - +
426B SER* 3.1 26.3 + - - -
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 3.9 21.4 - - - -
152B SER* 3.4 48.4 + - - +
153B LEU* 3.9 17.7 - - + +
154B LYS* 5.7 0.5 + - - -
408B VAL* 4.9 1.4 - - - +
412B SER* 3.3 29.5 + - - +
419B LEU* 2.9 37.6 + - - +
420B SER* 3.8 7.3 - - - +
422B PHE* 1.3 74.9 - - - +
424B ARG* 1.3 64.0 + - + +
426B SER* 4.1 4.6 - - - -
427B ASP* 3.4 21.5 + - - +
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Residues in contact with ARG 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B SER* 2.9 23.5 + - - +
421B LEU* 3.7 7.0 - - - +
422B PHE 3.3 0.2 - - - -
423B ARG* 1.3 76.6 - - - +
425B LEU* 1.3 64.4 + - - +
427B ASP* 3.3 6.4 + - - +
428B GLN* 3.3 30.1 + - + +
495B LEU* 3.1 40.5 + - - +
496B LEU* 3.9 25.4 - - + +
504B GLU* 3.4 29.9 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLN* 3.9 10.8 - - + +
354B LEU* 3.5 54.1 - - + +
357B PHE* 3.6 27.4 - - + +
358B THR* 5.3 1.6 - - + -
421B LEU* 3.0 39.2 + - + +
422B PHE 4.0 0.7 - - - +
424B ARG* 1.3 75.6 - - - +
426B SER* 1.3 58.3 + - - +
428B GLN* 3.5 6.2 + - - +
429B ARG* 3.0 29.6 + - - +
435B LEU* 5.7 0.2 - - - +
496B LEU* 3.9 23.1 - - + -
522B LEU* 4.6 8.1 - - + -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY* 5.8 1.0 - - - -
122B ALA* 5.2 4.7 + - - +
153B LEU 2.8 28.6 + - - -
154B LYS* 3.6 14.8 + - - +
357B PHE* 3.6 25.0 - - - -
422B PHE* 3.1 20.5 + - - -
423B ARG* 4.3 4.3 - - - -
425B LEU* 1.3 75.8 - - - +
427B ASP* 1.3 61.7 + - - +
429B ARG* 3.8 2.9 - - - +
430B SER* 3.0 28.3 + - - -
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LYS* 2.7 36.1 + - - +
423B ARG 3.4 16.1 + - - +
424B ARG* 3.3 7.7 + - - +
425B LEU 3.3 0.4 - - - -
426B SER* 1.3 78.2 - - - +
428B GLN* 1.3 62.5 + - + +
430B SER* 3.2 15.8 + - - -
431B LYS* 3.2 40.9 + - - +
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ARG* 3.3 16.5 + - + +
425B LEU* 3.8 8.5 - - - +
427B ASP* 1.3 75.3 + - + +
429B ARG* 1.3 66.3 + - - +
430B SER 3.1 1.4 + - - -
431B LYS* 3.1 25.2 + - - +
432B GLU* 3.1 46.4 + - - +
435B LEU* 3.9 15.1 - - + +
462B PHE* 4.0 7.6 - - - -
495B LEU* 3.5 38.8 - - + +
496B LEU* 6.1 3.4 - - + -
522B LEU* 5.0 9.0 - - + -
524B ARG* 5.1 4.0 + - - +
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Residues in contact with ARG 429 (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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119B HIS 3.1 28.9 + - - -
120B THR 3.7 1.6 - - - -
121B GLY* 3.6 25.1 + - - +
329B TRP* 3.8 9.3 - - - -
356B LEU 5.7 0.2 + - - -
357B PHE* 3.4 42.8 + - + +
359B LEU 4.9 3.8 + - - -
361B GLY 3.0 33.3 + - - +
362B THR* 4.1 1.0 - - - +
363B PRO* 4.1 12.8 - - + +
425B LEU 3.0 18.9 + - - +
426B SER* 3.8 4.7 - - - +
428B GLN* 1.3 75.4 - - - +
430B SER* 1.3 57.5 + - - +
435B LEU* 3.7 31.4 + - - +
436B LEU* 3.3 23.2 + - - +
454B ARG* 5.2 0.4 - - - +
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Residues in contact with SER 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.2 26.8 - - - +
121B GLY* 4.8 3.1 - - - -
154B LYS* 3.7 20.4 - - - +
156B LYS* 4.1 18.5 + - - -
426B SER 3.0 18.4 + - - -
427B ASP 3.2 8.0 + - - -
428B GLN 3.1 0.2 - - - -
429B ARG* 1.3 75.7 - - - +
431B LYS* 1.3 59.1 + - - +
436B LEU* 4.0 13.7 - - - +
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Residues in contact with LYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ASP* 3.2 35.0 + - - +
428B GLN* 3.1 39.0 + - - +
430B SER* 1.3 81.2 - - - +
432B GLU* 1.3 75.9 + - + +
433B ARG* 3.9 4.9 + - - +
436B LEU* 4.3 7.4 - - - +
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLN* 3.1 25.5 + - - +
431B LYS* 1.3 90.3 + - + +
433B ARG* 1.3 63.1 + - - +
434B SER 3.4 0.4 + - - -
435B LEU* 3.4 8.1 + - + +
436B LEU* 3.0 29.5 + - - +
459B ASN* 5.7 2.9 - - - +
460B GLU* 4.7 12.9 + - - +
462B PHE* 3.7 33.2 - - + -
524B ARG* 3.7 24.6 + - - -
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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
------------------------------------------------------------
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