Contacts of the helix formed by residues 535 - 549 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B THR* 4.9 20.0 - - + +
382B MET* 3.6 15.1 - - - -
534B THR* 1.3 82.5 + - - +
536B ARG* 1.3 54.4 + - - +
537B GLU* 3.0 14.9 + - - +
538B GLU* 2.7 49.5 + - - +
539B LEU* 2.8 35.0 + - - +
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Residues in contact with ARG 536 (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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372B LEU 2.9 20.8 + - - -
373B ALA* 3.6 3.7 - - - +
374B ASP* 2.8 36.2 + - - +
375B PRO* 4.8 6.1 - - - +
376B GLU 5.9 0.2 - - - -
382B MET* 3.5 20.5 - - + +
386B GLN* 3.4 32.0 + - + +
389B ASP* 2.6 31.3 + - - +
390B SER* 4.1 11.0 + - - +
535B ASN* 1.3 75.0 - - - +
537B GLU* 1.3 57.2 + - - +
539B LEU* 3.8 2.8 - - - +
540B LEU* 2.9 43.4 + - + +
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ASN* 3.0 12.3 + - - +
536B ARG* 1.3 75.0 - - - +
538B GLU* 1.3 66.7 + - + +
540B LEU* 4.1 6.1 - - - +
541B ALA* 3.2 24.6 + - + +
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Residues in contact with GLU 538 (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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532B ARG 4.4 5.2 - - - +
533B ALA* 3.7 15.7 - - + +
534B THR* 2.6 39.1 + - - +
535B ASN* 2.7 28.5 + - - +
537B GLU* 1.3 72.8 - - + +
539B LEU* 1.3 56.2 + - - +
541B ALA* 3.4 6.6 + - - +
542B ALA* 2.9 31.0 + - - +
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Residues in contact with LEU 539 (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 MET* 3.8 17.5 - - - -
387B VAL* 3.7 37.2 - - + +
390B SER* 3.7 20.2 - - - +
486B VAL* 4.6 8.3 - - + -
533B ALA* 3.6 9.1 - - + +
535B ASN 2.8 21.7 + - - +
536B ARG* 3.8 3.8 - - - +
538B GLU* 1.3 71.1 - - - +
540B LEU* 1.3 59.9 + - - +
542B ALA* 3.2 1.6 + - - +
543B LEU* 2.8 47.7 + - + +
555B ILE* 4.0 15.7 - - + -
557B VAL* 4.0 20.4 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER* 3.8 37.2 - - - +
393B THR* 4.1 17.5 - - + +
394B VAL* 3.9 10.8 - - + -
536B ARG* 2.9 30.8 + - + +
537B GLU* 4.1 6.5 - - - +
539B LEU* 1.3 72.0 - - - +
541B ALA* 1.3 57.5 + - - +
543B LEU* 3.4 4.6 + - - +
544B ARG* 2.9 60.0 + - - +
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Residues in contact with ALA 541 (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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537B GLU* 3.2 18.2 + - + +
538B GLU* 3.5 7.4 - - - +
540B LEU* 1.3 79.7 - - - +
542B ALA* 1.3 57.7 + - - +
544B ARG* 3.4 7.6 + - - +
545B LYS* 3.0 29.7 + - - +
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Residues in contact with ALA 542 (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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531B THR* 3.7 26.0 - - + -
533B ALA* 4.5 1.6 - - + -
538B GLU 2.9 17.9 + - - +
539B LEU* 3.6 4.7 - - - +
541B ALA* 1.3 77.0 - - - +
543B LEU* 1.3 56.9 + - - +
545B LYS* 3.5 5.2 + - - +
546B GLY* 2.9 24.8 + - - -
553B PHE* 3.5 13.2 - - - -
555B ILE* 3.7 25.1 - - + -
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER* 3.5 36.3 - - - +
391B MET* 3.7 10.5 - - + +
394B VAL* 3.7 20.1 - - + +
458B PHE* 4.2 20.2 - - + -
484B VAL* 4.2 12.2 - - + +
486B VAL* 3.9 17.9 - - + -
539B LEU* 2.8 39.0 + - + +
542B ALA* 1.3 72.4 - - - +
544B ARG* 1.3 58.0 + - - +
546B GLY* 3.3 1.0 + - - -
547B ALA* 2.8 31.4 + - - +
555B ILE* 3.7 19.7 - - + -
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Residues in contact with ARG 544 (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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393B THR* 3.8 15.6 - - - +
394B VAL* 3.8 17.0 - - + +
397B GLU* 2.7 40.4 + - - +
540B LEU* 2.9 54.6 + - - +
541B ALA* 3.8 6.2 - - - +
543B LEU* 1.3 74.4 - - - +
545B LYS* 1.3 65.2 + - - +
547B ALA* 3.5 1.9 + - - +
548B GLU* 3.3 32.8 + - - +
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Residues in contact with LYS 545 (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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529B ASP* 6.0 1.0 - - - +
530B ALA 5.6 0.8 + - - -
531B THR* 5.6 4.6 - - + -
541B ALA 3.0 17.9 + - - +
542B ALA* 3.6 6.7 - - - +
544B ARG* 1.3 73.3 - - - +
546B GLY* 1.3 66.1 + - - +
548B GLU* 3.2 5.9 + - - +
549B LEU* 3.0 40.2 + - + +
553B PHE* 4.0 32.0 - - + -
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Residues in contact with GLY 546 (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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482B PRO* 5.0 2.3 - - - +
484B VAL* 3.5 15.6 - - - +
542B ALA 2.9 12.1 + - - -
543B LEU 3.7 3.1 - - - -
545B LYS* 1.3 74.8 - - - +
547B ALA* 1.3 60.9 + - - +
549B LEU* 3.2 17.7 + - - +
550B GLY 4.6 0.9 + - - -
551B ARG 4.2 6.6 - - - +
553B PHE* 3.6 33.4 - - - -
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Residues in contact with ALA 547 (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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394B VAL* 4.2 10.5 - - + -
398B ALA* 4.1 27.0 - - + +
456B PRO* 5.9 1.7 - - + +
458B PHE* 4.3 10.5 - - + -
482B PRO 6.0 0.4 - - - -
484B VAL* 3.7 8.1 - - - +
543B LEU 2.8 20.6 + - - +
544B ARG* 3.8 5.2 - - - +
545B LYS 3.3 0.2 - - - -
546B GLY* 1.3 72.7 - - - +
548B GLU* 1.3 62.5 + - + +
550B GLY 5.1 1.2 + - - -
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Residues in contact with GLU 548 (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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544B ARG* 3.3 19.5 + - - +
545B LYS* 3.2 5.6 + - - +
547B ALA* 1.3 79.7 - - + +
549B LEU* 1.3 64.0 + - - +
550B GLY* 3.3 4.5 + - - -
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Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ASP* 4.1 4.3 - - + +
545B LYS* 3.0 28.9 + - + +
546B GLY* 3.2 15.0 + - - +
548B GLU* 1.3 78.0 - - - +
550B GLY* 1.3 59.4 + - - +
551B ARG* 3.1 53.4 + - + +
552B PRO 3.8 15.9 - - - +
553B PHE* 3.7 31.4 - - + -
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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