Contacts of the helix formed by residues 535 - 549 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377D THR* 5.7 9.6 - - + -
382D MET* 3.5 15.2 - - - -
533D ALA 3.6 0.6 - - - -
534D THR* 1.3 82.8 + - - +
536D ARG* 1.3 64.0 + - - +
537D GLU* 3.2 11.1 + - - +
538D GLU* 2.8 49.7 + - - +
539D LEU* 2.9 23.9 + - - +
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Residues in contact with ARG 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D LEU 2.8 24.0 + - - -
373D ALA* 3.6 5.1 - - - +
374D ASP 3.0 34.0 + - - +
375D PRO* 4.8 5.2 - - - +
382D MET* 3.6 19.7 - - + +
386D GLN* 3.5 31.6 + - + +
389D ASP* 2.9 28.1 + - - +
390D SER* 4.3 10.2 + - - +
535D ASN* 1.3 74.7 - - - +
537D GLU* 1.3 57.8 + - - +
539D LEU* 3.3 3.1 + - - +
540D LEU* 2.9 45.1 + - + +
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Residues in contact with GLU 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D ASN* 3.2 10.0 + - - +
536D ARG* 1.3 75.8 - - - +
538D GLU* 1.3 68.9 + - + +
540D LEU* 4.0 8.0 - - - +
541D ALA* 3.2 23.7 + - + +
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Residues in contact with GLU 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D ARG 4.3 5.5 - - - +
533D ALA* 3.7 13.9 - - - +
534D THR* 2.7 39.8 + - - +
535D ASN* 2.8 29.5 + - - +
537D GLU* 1.3 74.3 - - + +
539D LEU* 1.3 57.7 + - - +
541D ALA* 3.4 6.0 + - - +
542D ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D MET* 3.9 16.2 - - + -
387D VAL* 3.7 29.8 - - + +
390D SER* 3.5 28.5 - - - +
486D VAL* 4.5 9.0 - - + -
533D ALA* 3.6 9.4 - - + +
535D ASN 2.9 18.0 + - - +
536D ARG 3.8 3.6 - - - +
538D GLU* 1.3 74.3 - - - +
540D LEU* 1.3 60.7 + - - +
542D ALA* 3.3 1.0 + - - +
543D LEU* 2.9 44.2 + - + +
555D ILE* 3.9 14.4 - - + -
557D VAL* 3.9 21.5 - - + -
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Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D SER* 3.8 38.1 - - - +
393D THR* 4.2 15.7 - - + -
394D VAL* 3.8 13.9 - - + +
536D ARG* 2.9 31.8 + - + +
537D GLU* 4.0 6.5 - - - +
539D LEU* 1.3 77.1 - - - +
541D ALA* 1.3 61.0 + - - +
543D LEU* 3.4 1.5 + - - +
544D ARG* 3.0 54.0 + - - +
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Residues in contact with ALA 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D GLU* 3.2 18.8 + - + +
538D GLU* 3.7 6.5 - - - +
540D LEU* 1.3 76.2 - - - +
542D ALA* 1.3 58.2 + - - +
544D ARG* 3.5 7.0 + - - +
545D LYS* 3.0 30.8 + - - +
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Residues in contact with ALA 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D THR* 3.7 27.8 - - + -
533D ALA* 4.5 1.6 - - + -
538D GLU 2.9 18.3 + - - +
539D LEU* 3.6 4.9 - - - +
541D ALA* 1.3 77.6 - - - +
543D LEU* 1.3 55.5 + - - +
545D LYS* 3.5 4.1 + - - +
546D GLY 2.9 23.2 + - - -
553D PHE* 3.3 16.5 - - - -
555D ILE* 3.7 23.3 - - + -
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Residues in contact with LEU 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D SER* 3.7 33.7 - - - +
391D MET* 3.7 15.0 - - + +
394D VAL* 3.8 19.0 - - + +
458D PHE* 4.4 16.8 - - + -
484D VAL* 4.0 14.8 - - + +
486D VAL* 3.9 25.1 - - + -
539D LEU* 2.9 36.9 + - + +
540D LEU* 3.9 0.7 - - - +
542D ALA* 1.3 73.6 - - - +
544D ARG* 1.3 55.5 + - - +
546D GLY* 3.2 0.9 + - - -
547D ALA* 2.7 36.9 + - - +
555D ILE* 3.9 12.1 - - + -
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Residues in contact with ARG 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D THR* 4.1 13.9 - - - +
394D VAL* 3.8 17.9 - - + +
397D GLU* 2.8 39.8 + - - +
540D LEU* 3.0 52.3 + - - +
541D ALA* 3.9 6.6 - - - +
543D LEU* 1.3 72.4 - - - +
545D LYS* 1.3 67.1 + - - +
547D ALA* 3.4 2.4 + - - +
548D GLU* 3.3 32.6 + - - +
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Residues in contact with LYS 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D ASP* 6.1 1.1 - - - -
531D THR* 5.8 3.0 - - + -
541D ALA 3.0 19.2 + - - +
542D ALA* 3.6 5.2 - - - +
544D ARG* 1.3 78.3 - - - +
546D GLY* 1.3 63.8 + - - +
548D GLU* 3.3 3.4 + - - +
549D LEU* 3.1 40.7 + - + +
553D PHE* 3.8 33.7 - - + -
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Residues in contact with GLY 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D PRO* 5.1 2.8 - - - +
484D VAL* 3.5 16.6 - - - +
542D ALA 2.9 11.7 + - - -
543D LEU 3.2 3.3 + - - -
545D LYS* 1.3 76.4 - - - +
547D ALA* 1.3 61.9 + - - +
549D LEU* 3.2 16.3 + - - +
550D GLY 4.6 0.7 + - - -
551D ARG 4.3 5.9 - - - +
553D PHE* 3.6 33.2 - - - -
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Residues in contact with ALA 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D VAL* 4.2 11.7 - - + -
398D ALA* 4.0 27.4 - - + +
456D PRO* 5.9 2.2 - - + +
458D PHE* 4.2 10.1 - - + -
484D VAL* 3.8 8.7 - - - +
543D LEU 2.7 19.8 + - - +
544D ARG* 3.8 6.1 - - - +
545D LYS 3.3 0.2 - - - -
546D GLY* 1.3 72.8 - - - +
548D GLU* 1.3 63.3 + - + +
549D LEU 3.5 0.4 + - - -
550D GLY 5.1 1.2 + - - -
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Residues in contact with GLU 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D ARG* 3.3 18.0 + - - +
545D LYS* 3.3 6.0 + - - +
546D GLY 3.2 0.8 - - - -
547D ALA* 1.3 80.6 - - + +
549D LEU* 1.3 62.0 + - - +
550D GLY* 3.3 3.6 + - - -
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Residues in contact with LEU 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D ASP* 4.1 4.5 - - - +
545D LYS* 3.1 31.9 + - + +
546D GLY* 3.2 12.0 + - - +
548D GLU* 1.3 79.1 - - - +
550D GLY* 1.3 60.7 + - - +
551D ARG* 3.1 53.5 + - + +
552D PRO 3.9 15.5 - - - +
553D PHE* 3.7 31.6 - - + -
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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
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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