Contacts of the helix formed by residues 535 - 548 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C THR* 4.6 26.4 - - + +
382C MET* 3.6 15.6 - - - -
533C ALA 3.7 0.4 - - - -
534C THR* 1.3 89.1 + - - +
536C ARG* 1.3 55.9 + - - +
537C GLU* 3.3 12.6 + - - +
538C GLU* 3.0 33.0 + - - +
539C LEU* 2.8 32.9 + - - +
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Residues in contact with ARG 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C LEU 2.7 23.6 + - - -
373C ALA* 3.5 8.8 + - - +
374C ASP* 2.8 31.8 + - - +
375C PRO* 4.6 7.8 - - - +
376C GLU 5.8 0.2 - - - -
382C MET* 3.5 20.7 - - + +
386C GLN* 3.5 33.9 + - + +
389C ASP* 2.7 31.1 + - - +
390C SER* 4.2 10.4 + - - +
535C ASN* 1.3 73.1 - - - +
537C GLU* 1.3 57.3 + - - +
539C LEU* 4.4 2.0 - - - -
540C LEU* 2.8 43.7 + - + +
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Residues in contact with GLU 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C ASN* 3.2 12.2 + - - +
536C ARG* 1.3 79.7 - - - +
538C GLU* 1.3 65.0 + - + +
540C LEU* 4.1 7.0 - - - +
541C ALA* 3.3 23.4 + - - +
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Residues in contact with GLU 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C ARG 4.1 6.4 - - - +
533C ALA* 3.6 9.8 - - - +
534C THR* 2.7 49.9 + - - +
535C ASN* 3.0 26.2 + - - +
537C GLU* 1.3 79.3 - - + +
539C LEU* 1.3 57.3 + - - +
541C ALA* 3.6 5.0 + - - +
542C ALA* 3.0 28.4 + - - +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C MET* 3.9 17.5 - - + -
387C VAL* 3.7 31.4 - - + +
390C SER* 3.7 22.2 - - - +
391C MET* 5.6 0.2 - - + -
486C VAL* 4.4 9.0 - - + -
533C ALA* 3.6 9.1 - - + +
535C ASN 2.8 21.0 + - - +
536C ARG* 3.9 3.6 - - - +
538C GLU* 1.3 69.9 - - - +
540C LEU* 1.3 67.5 + - - +
542C ALA* 3.1 1.4 + - - +
543C LEU* 2.8 48.1 + - + +
555C ILE* 4.0 14.4 - - + -
557C VAL* 4.0 20.4 - - + -
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C SER* 3.8 36.8 - - - +
393C THR* 4.0 16.8 - - + -
394C VAL* 3.8 15.3 - - + +
536C ARG* 2.8 33.3 + - + +
537C GLU* 4.1 5.8 - - - +
539C LEU* 1.3 72.5 - - - +
541C ALA* 1.3 56.3 + - - +
543C LEU* 3.8 2.3 - - - +
544C ARG* 3.0 57.5 + - - +
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Residues in contact with ALA 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C GLU 3.3 15.6 + - - +
538C GLU* 3.8 6.5 - - - +
539C LEU 3.2 0.6 - - - -
540C LEU* 1.3 77.6 - - - +
542C ALA* 1.3 58.5 + - - +
544C ARG* 3.5 8.9 + - - +
545C LYS* 3.0 30.0 + - - +
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Residues in contact with ALA 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C THR* 3.6 29.6 - - + -
533C ALA* 4.5 1.6 - - + -
538C GLU 3.0 18.6 + - - +
539C LEU 3.6 3.8 - - - +
541C ALA* 1.3 77.6 - - - +
543C LEU* 1.3 56.1 + - - +
545C LYS* 3.4 4.5 + - - +
546C GLY 3.0 23.4 + - - -
553C PHE* 3.5 14.7 - - - -
555C ILE* 3.7 21.1 - - + -
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Residues in contact with LEU 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C SER* 3.7 33.9 - - - +
391C MET* 3.8 13.2 - - + +
394C VAL* 3.7 20.0 - - + +
458C PHE* 4.1 23.8 - - + -
484C VAL* 4.1 10.5 - - + +
486C VAL* 4.0 23.8 - - + -
539C LEU* 2.8 43.3 + - + +
540C LEU 3.8 0.2 - - - +
542C ALA* 1.3 71.6 - - - +
544C ARG* 1.3 59.6 + - - +
546C GLY* 3.3 1.0 + - - -
547C ALA* 2.9 31.9 + - - +
555C ILE* 4.0 7.6 - - + -
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Residues in contact with ARG 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C THR* 4.0 12.9 - - - +
394C VAL* 3.9 12.7 - - + +
397C GLU* 2.7 44.4 + - - +
540C LEU* 3.0 51.2 + - - +
541C ALA* 3.8 8.0 - - - +
543C LEU* 1.3 75.6 - - - +
545C LYS* 1.3 62.3 + - - +
547C ALA* 3.5 2.2 + - - +
548C GLU* 3.4 35.5 + - - +
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Residues in contact with LYS 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C THR* 5.9 2.0 - - + -
541C ALA 3.0 17.2 + - - +
542C ALA* 3.7 6.1 - - - +
544C ARG* 1.3 77.0 - - - +
546C GLY* 1.3 61.7 + - - +
548C GLU* 3.3 5.4 + - - +
549C LEU* 3.1 40.1 + - + +
553C PHE* 4.0 31.5 - - + -
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Residues in contact with GLY 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C PRO* 5.0 2.4 - - - +
484C VAL* 3.5 16.2 - - - +
542C ALA 3.0 11.7 + - - -
543C LEU 3.3 3.1 + - - -
545C LYS* 1.3 76.6 - - - +
547C ALA* 1.3 61.7 + - - +
548C GLU 3.2 1.2 + - - -
549C LEU* 3.2 15.9 + - - +
550C GLY 4.6 0.9 + - - -
551C ARG 4.3 6.2 - - - +
553C PHE* 3.7 31.8 - - - -
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Residues in contact with ALA 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C VAL* 4.2 6.3 - - + -
398C ALA* 4.0 27.0 - - + +
456C PRO* 5.7 3.0 - - + +
458C PHE* 4.1 15.9 - - + -
484C VAL* 3.8 9.0 - - - +
543C LEU 2.9 16.8 + - - +
544C ARG* 3.9 5.6 - - - +
545C LYS 3.3 0.2 - - - -
546C GLY* 1.3 75.0 - - - +
548C GLU* 1.3 62.7 + - + +
549C LEU 3.5 0.2 - - - -
550C GLY 5.1 1.6 + - - -
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Residues in contact with GLU 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C ALA* 6.4 0.7 - - + -
544C ARG* 3.4 19.9 + - - +
545C LYS* 3.3 5.8 + - - +
546C GLY 3.1 0.4 - - - -
547C ALA* 1.3 81.0 - - + +
549C LEU* 1.3 62.1 + - - +
550C GLY* 3.4 3.7 + - - -
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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