Contacts of the helix formed by residues 535 - 549 (chain A) in PDB entry 2IHU
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 ASN 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A THR* 5.6 11.4 - - + +
382A MET* 3.6 14.7 - - - -
533A ALA 3.7 0.6 - - - -
534A THR* 1.3 83.3 + - - +
536A ARG* 1.3 60.0 + - - +
537A GLU* 3.2 13.2 + - - +
538A GLU* 2.7 51.4 + - - +
539A LEU* 2.8 28.8 + - - +
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Residues in contact with ARG 536 (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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372A LEU 2.9 22.8 + - - -
373A ALA* 3.6 4.1 - - - -
374A ASP 2.8 34.9 + - - +
375A PRO* 4.7 6.2 - - - +
376A GLU 5.9 0.9 - - - +
382A MET* 3.7 19.8 - - + +
386A GLN* 3.5 31.9 + - + +
389A ASP* 2.7 30.3 + - - +
390A SER* 4.2 10.3 + - - +
535A ASN* 1.3 75.0 - - - +
537A GLU* 1.3 57.4 - - - +
539A LEU* 3.8 2.8 - - - +
540A LEU* 2.9 44.5 + - + +
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Residues in contact with GLU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASN* 3.2 13.0 + - - +
536A ARG* 1.3 78.8 - - - +
538A GLU* 1.3 64.0 + - + +
540A LEU* 3.6 7.1 + - - +
541A ALA* 3.2 23.9 + - - +
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Residues in contact with GLU 538 (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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532A ARG 4.1 5.0 - - - +
533A ALA* 3.6 16.1 - - + +
534A THR* 2.7 45.1 + - - +
535A ASN* 2.7 30.1 + - - +
537A GLU* 1.3 75.1 - - + +
539A LEU* 1.3 58.4 + - - +
541A ALA* 3.5 6.0 + - - +
542A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 539 (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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382A MET* 4.0 15.0 - - + -
387A VAL* 3.7 33.2 - - + +
390A SER* 3.7 21.8 - - - +
391A MET* 5.5 0.2 - - + -
486A VAL* 4.6 7.6 - - + -
533A ALA* 3.6 6.4 - - + +
535A ASN 2.8 17.1 + - - +
536A ARG* 3.8 4.0 - - - +
538A GLU* 1.3 74.9 - - - +
540A LEU* 1.3 61.1 + - - +
542A ALA* 3.2 2.0 + - - +
543A LEU* 2.8 53.2 + - + +
555A ILE* 3.9 16.8 - - + -
557A VAL* 3.9 21.3 - - + -
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Residues in contact with LEU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.8 35.9 - - - +
393A THR* 4.0 17.7 - - + +
394A VAL* 3.8 15.0 - - + -
536A ARG* 2.9 32.8 + - + +
537A GLU* 4.1 5.4 - - - +
539A LEU* 1.3 72.4 - - - +
541A ALA* 1.3 57.6 + - - +
543A LEU* 3.4 2.1 + - - +
544A ARG* 3.0 59.2 + - - +
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Residues in contact with ALA 541 (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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537A GLU* 3.2 16.8 + - + +
538A GLU* 3.7 6.5 - - - +
540A LEU* 1.3 79.3 - - - +
542A ALA* 1.3 56.2 + - - +
544A ARG* 3.9 7.8 - - - +
545A LYS* 3.0 29.5 + - - +
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Residues in contact with ALA 542 (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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531A THR* 3.7 26.7 - - + -
533A ALA* 4.5 1.6 - - + -
538A GLU 3.0 18.5 + - - +
539A LEU 3.6 3.6 - - - +
541A ALA* 1.3 76.1 - - - +
543A LEU* 1.3 57.1 + - - +
545A LYS* 3.4 4.5 + - - +
546A GLY 2.9 24.3 + - - -
553A PHE* 3.4 14.6 - - - -
555A ILE* 3.6 26.5 - - + -
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Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.6 35.2 - - - +
391A MET* 3.7 13.5 - - + +
394A VAL* 3.7 19.8 - - + +
458A PHE* 4.3 15.5 - - + -
484A VAL* 4.1 14.0 - - + +
486A VAL* 3.8 18.4 - - + -
539A LEU* 2.8 39.0 + - + +
542A ALA* 1.3 73.1 - - - +
544A ARG* 1.3 58.6 + - - +
546A GLY* 3.3 0.9 + - - -
547A ALA* 2.8 31.4 + - - +
555A ILE* 3.8 19.5 - - + -
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Residues in contact with ARG 544 (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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393A THR* 3.9 15.2 - - - +
394A VAL* 3.8 15.0 - - + +
397A GLU* 2.8 43.2 + - - +
540A LEU* 3.0 51.6 + - - +
541A ALA* 3.9 6.3 - - - +
543A LEU* 1.3 71.5 - - - +
545A LYS* 1.3 65.1 + - - +
547A ALA* 4.0 2.3 - - - +
548A GLU* 3.3 37.2 + - - +
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Residues in contact with LYS 545 (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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529A ASP* 6.2 0.8 - - - +
531A THR* 5.6 4.7 - - + -
541A ALA 3.0 18.1 + - - +
542A ALA* 3.5 7.4 - - - +
544A ARG* 1.3 77.0 - - - +
546A GLY* 1.3 60.6 + - - +
548A GLU* 3.4 4.8 + - - +
549A LEU* 3.2 39.6 + - + +
553A PHE* 4.0 31.1 - - + -
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Residues in contact with GLY 546 (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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482A PRO* 5.0 2.4 - - - +
484A VAL* 3.4 17.4 - - - +
542A ALA 2.9 11.9 + - - -
543A LEU 3.7 2.9 - - - -
545A LYS* 1.3 76.2 - - - +
547A ALA* 1.3 62.1 + - - +
549A LEU* 3.2 17.7 + - - +
550A GLY 4.6 0.9 + - - -
551A ARG 4.3 4.7 - - - +
553A PHE* 3.6 32.1 - - - -
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Residues in contact with ALA 547 (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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394A VAL* 4.2 6.5 - - + -
398A ALA* 4.1 27.3 - - + +
456A PRO* 5.8 1.7 - - + +
458A PHE* 4.2 15.5 - - + -
484A VAL* 3.7 7.7 - - - +
543A LEU 2.8 17.0 + - - +
544A ARG* 4.0 4.9 - - - +
546A GLY* 1.3 75.7 - - - +
548A GLU* 1.3 62.4 + - + +
549A LEU 3.4 0.4 + - - -
550A GLY 5.1 1.2 + - - -
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Residues in contact with GLU 548 (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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544A ARG* 3.3 22.7 + - - +
545A LYS* 3.8 4.7 - - - +
546A GLY 3.2 0.6 - - - -
547A ALA* 1.3 78.6 - - + +
549A LEU* 1.3 61.6 + - - +
550A GLY* 3.4 3.5 + - - -
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASP* 4.3 4.7 - - + +
545A LYS* 3.2 35.9 + - + +
546A GLY 3.2 11.8 + - - +
547A ALA 3.4 0.4 - - - -
548A GLU* 1.3 78.3 - - - +
550A GLY* 1.3 62.1 + - - +
551A ARG* 3.1 51.8 + - + +
552A PRO 3.6 23.6 - - - +
553A PHE* 3.7 23.1 - - + -
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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