Contacts of the helix formed by residues 417 - 432 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.5 10.0 + - - +
411A GLN* 2.8 46.4 + - - +
414A ASP* 3.1 20.9 + - - -
415A PRO 3.2 2.2 - - - +
416A GLY* 1.3 82.1 - - - +
418A LEU* 1.3 63.4 + - - +
419A LEU 3.5 1.7 + - - -
420A SER* 3.2 14.4 + - - -
421A LEU 3.3 15.8 + - - -
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.0 17.9 - - + -
350A ARG* 3.7 40.9 - - + +
353A GLN* 3.7 31.0 - - - +
369A ASP 4.3 0.4 - - - +
370A GLU 3.5 5.6 - - - +
371A ILE 3.9 2.2 - - - +
372A GLY* 3.6 33.9 - - - +
411A GLN* 4.1 9.2 + - - +
417A SER* 1.3 72.4 - - - +
419A LEU* 1.3 60.4 + - - +
421A LEU* 3.3 9.3 + - + +
422A PHE* 3.0 27.2 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 4.4 3.6 - - - +
153A LEU* 4.2 13.7 - - + -
370A GLU* 3.2 36.6 + - + +
371A ILE* 4.4 2.7 - - + -
408A VAL* 3.7 22.7 - - + +
411A GLN* 3.4 23.9 + - + +
412A SER* 3.5 22.9 - - - +
417A SER* 3.8 0.7 - - - +
418A LEU* 1.3 79.8 - - - +
420A SER* 1.3 59.3 + - - +
422A PHE* 3.5 2.0 + - + +
423A ARG* 3.1 59.0 + - - +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLN 4.1 3.3 + - - -
412A SER 5.4 1.7 + - - -
414A ASP 3.1 19.2 + - - -
415A PRO* 3.1 29.8 + - - +
417A SER* 3.2 12.8 + - - -
418A LEU 3.3 0.2 - - - -
419A LEU* 1.3 75.6 - - - +
421A LEU* 1.3 65.2 + - - +
423A ARG* 3.5 10.0 + - - +
424A ARG* 3.2 35.5 + - - +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.6 61.0 - - + +
353A GLN* 4.6 3.8 - - - +
354A LEU* 5.9 0.2 - - + -
417A SER 3.3 10.4 + - - +
418A LEU* 3.3 13.7 + - + +
420A SER* 1.3 80.3 - - - +
422A PHE* 1.3 56.6 + - - +
424A ARG* 3.3 6.1 + - - +
425A LEU* 2.9 49.2 + - + +
496A LEU* 3.8 36.8 - - + -
497A SER 4.8 7.2 - - - +
498A THR* 4.7 6.5 - - + -
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA* 5.9 0.2 - - + -
124A TYR* 5.4 4.0 - + - -
153A LEU* 4.1 38.4 - - + -
155A VAL* 5.1 7.9 - - + -
353A GLN* 3.4 28.2 + - - +
357A PHE* 3.8 30.3 - + - -
365A PHE* 4.0 32.3 - + + -
369A ASP 4.9 0.2 - - - -
370A GLU* 3.8 37.0 - - + +
418A LEU 3.0 17.5 + - - +
419A LEU* 3.7 6.7 - - + +
420A SER 3.3 0.2 - - - -
421A LEU* 1.3 76.7 - - - +
423A ARG* 1.3 61.6 + - - +
425A LEU* 3.8 4.3 - - - +
426A SER* 2.9 33.1 + - - -
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Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 4.2 14.5 - - - -
152A SER* 3.5 46.4 + - - +
153A LEU* 4.2 12.6 - - + +
154A LYS* 4.5 7.0 + - - +
408A VAL* 4.8 0.8 - - - +
411A GLN 5.0 0.6 + - - -
412A SER* 3.5 30.1 + - - +
419A LEU* 3.1 50.5 + - + +
420A SER* 3.9 8.7 + - - +
421A LEU 3.3 0.4 - - - -
422A PHE* 1.3 81.7 - - - +
424A ARG* 1.3 58.4 + - + +
426A SER* 3.7 3.6 + - - -
427A ASP* 3.1 28.1 + - - +
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PRO 5.5 4.4 + - - -
420A SER* 3.2 25.4 + - - +
421A LEU* 3.7 4.9 - - - +
423A ARG* 1.3 75.9 - - + +
425A LEU* 1.3 66.8 + - - +
427A ASP* 3.3 7.0 + - - +
428A GLN* 3.2 28.1 + - - +
495A LEU* 3.5 20.8 + - - +
496A LEU* 4.0 25.9 - - + +
504A GLU* 3.5 32.1 + - - +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLN* 3.9 10.5 - - + +
354A LEU* 3.5 55.4 - - + +
357A PHE* 3.9 21.7 - - + +
358A THR* 5.3 2.0 - - + -
421A LEU* 2.9 40.3 + - + +
422A PHE 3.9 3.1 - - - +
424A ARG* 1.3 75.6 - - - +
426A SER* 1.3 57.3 + - - +
428A GLN* 3.4 7.0 + - + +
429A ARG* 3.1 27.4 + - - +
496A LEU* 4.2 13.9 - - + -
522A LEU* 4.0 18.6 - - + -
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Residues in contact with SER 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA* 4.8 4.3 + - - +
153A LEU 2.7 29.1 + - - -
154A LYS* 3.7 12.1 + - - +
357A PHE* 3.5 29.3 - - - -
422A PHE* 2.9 20.8 + - - -
423A ARG 4.0 3.6 - - - -
425A LEU* 1.3 74.0 - - - +
427A ASP* 1.3 62.9 + - - +
429A ARG* 3.5 1.9 + - - +
430A SER* 2.8 27.7 + - - -
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Residues in contact with ASP 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LYS* 2.8 43.7 + - - +
423A ARG 3.1 14.7 + - - +
424A ARG* 3.7 8.3 - - - +
425A LEU 3.3 0.4 - - - -
426A SER* 1.3 74.7 - - - +
428A GLN* 1.3 68.4 + - + +
430A SER* 3.2 2.8 + - - -
431A LYS* 2.8 68.6 + - - +
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Residues in contact with GLN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ARG 3.2 13.7 + - - +
425A LEU* 3.6 9.4 - - - +
427A ASP* 1.3 81.6 - - - +
429A ARG* 1.3 64.0 + - - +
430A SER 3.0 0.3 + - - -
431A LYS* 3.3 3.2 + - - +
432A GLU* 3.0 65.7 + - - +
435A LEU* 4.3 14.1 - - + +
462A PHE* 4.0 6.2 - - + -
495A LEU* 3.7 39.0 - - + +
496A LEU* 6.5 1.3 - - + -
522A LEU* 5.0 6.1 - - + -
524A ARG* 4.4 4.8 + - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A HIS 3.2 29.5 + - - -
120A THR 4.0 3.6 - - - -
121A GLY* 4.4 17.1 + - - +
329A TRP* 4.0 8.5 - - - -
356A LEU 5.6 0.2 + - - -
357A PHE* 3.3 44.5 + - + +
358A THR* 5.5 0.2 - - - +
359A LEU 5.1 3.0 + - - -
361A GLY 2.9 32.7 + - - -
362A THR* 4.2 5.3 - - - +
363A PRO* 4.2 9.9 - - + +
425A LEU 3.1 14.5 + - - +
426A SER 3.6 6.3 - - - +
427A ASP 3.4 0.2 - - - -
428A GLN* 1.3 79.0 - - - +
430A SER* 1.3 60.6 + - - +
432A GLU 4.1 2.3 - - - +
435A LEU* 3.2 37.3 + - - +
436A LEU* 3.7 15.7 - - - +
454A ARG* 6.2 0.2 - - - +
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Residues in contact with SER 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 3.5 20.2 - - - +
121A GLY* 5.1 1.6 - - - -
154A LYS* 4.0 16.1 - - - +
156A LYS* 3.9 22.0 - - - -
426A SER 2.8 18.8 + - - -
427A ASP* 3.2 13.2 + - - -
429A ARG* 1.3 77.4 - - - +
431A LYS* 1.3 63.7 + - - +
436A LEU* 3.4 22.0 - - - +
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Residues in contact with LYS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LYS* 4.7 2.7 - - - +
427A ASP* 2.8 51.8 + - - +
428A GLN* 4.3 2.2 - - - +
430A SER* 1.3 79.3 - - - +
432A GLU* 1.3 68.3 + - + +
433A ARG* 3.8 8.1 + - - +
436A LEU* 4.0 5.2 - - - +
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A GLN* 3.0 43.8 + - - +
429A ARG 4.1 2.8 - - - +
431A LYS* 1.3 79.2 - - + +
433A ARG* 1.3 65.2 + - - +
434A SER 3.6 0.3 + - - -
435A LEU* 3.6 6.8 + - + -
436A LEU* 3.2 23.5 + - - +
459A ASN* 6.2 0.2 - - - +
460A GLU* 4.2 11.8 - - - +
462A PHE* 3.7 30.7 - - + -
524A ARG* 3.9 18.2 + - - -
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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