Contacts of the helix formed by residues 552 - 561 (chain D) in PDB entry 5ED1
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 HIS 552 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D SER* 3.2 33.1 - - - -
457D PHE* 4.2 22.9 - + + -
459D PRO* 6.2 0.4 - - + -
461D GLU 5.5 3.3 + - - -
463D ILE* 3.4 30.7 + - + +
550D LEU 3.5 3.4 + - - -
551D TYR* 1.3 77.9 - - - +
553D GLY* 1.3 61.1 + - - +
554D ASP* 3.3 39.6 + - + +
555D HIS* 3.6 25.9 - + + -
556D LEU* 2.9 35.8 + - - +
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Residues in contact with GLY 553 (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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305D PRO 6.0 0.4 - - - -
306D SER* 3.3 15.7 + - - -
308D GLN 4.7 2.0 - - - -
310D ILE* 3.9 21.5 - - - +
551D TYR* 3.7 23.4 - - - -
552D HIS* 1.3 71.0 + - - +
554D ASP* 1.3 51.2 + - - +
556D LEU* 4.2 1.3 - - - +
557D SER* 2.7 40.8 + - - -
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Residues in contact with ASP 554 (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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306D SER* 5.4 2.7 - - - +
310D ILE* 5.9 0.9 - - - +
463D ILE* 3.5 26.9 - - + +
465D GLU* 6.1 1.3 - - + -
552D HIS* 3.3 25.7 + - + +
553D GLY* 1.3 75.7 - - - +
555D HIS* 1.3 62.2 + - + +
557D SER* 2.9 19.0 + - - -
558D ARG* 3.0 15.8 + - - +
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Residues in contact with HIS 555 (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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453D ASP 4.8 0.4 - - - +
454D ALA* 4.3 17.0 - - - +
456D ILE 4.3 3.3 + - - -
457D PHE* 3.4 39.7 - + + +
463D ILE* 3.3 29.5 - - + +
465D GLU* 4.8 3.4 - - + -
477D ARG* 5.1 7.6 - - - -
552D HIS* 3.4 38.1 + + + +
554D ASP* 1.3 79.0 - - + +
556D LEU* 1.3 58.8 - - - +
558D ARG* 2.9 45.5 + - - +
559D ALA* 2.9 29.4 + - - +
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Residues in contact with LEU 556 (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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449D SER* 4.4 1.1 - - - +
450D PRO* 4.2 6.1 - - + -
454D ALA* 4.0 23.7 + - + +
545D ILE* 5.0 4.0 - - + +
547D LEU* 3.5 38.6 - - + -
551D TYR* 3.6 23.8 - - + -
552D HIS 2.9 19.8 + - - +
553D GLY* 4.2 1.3 - - - +
555D HIS* 1.3 74.6 - - - +
557D SER* 1.3 59.5 + - - +
559D ALA* 3.2 2.6 + - - +
560D MET* 2.9 54.1 + - + +
581D LEU* 3.8 24.5 - - + -
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Residues in contact with SER 557 (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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310D ILE* 4.8 10.0 - - - +
553D GLY 2.7 26.2 + - - -
554D ASP* 2.9 15.6 + - - -
556D LEU* 1.3 72.9 - - - +
558D ARG* 1.3 65.4 + - - +
561D TYR* 3.3 28.0 + - - -
562D GLN* 2.9 25.9 + - - +
581D LEU* 3.6 17.6 - - - +
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Residues in contact with ARG 558 (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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453D ASP* 2.6 44.7 + - - +
456D ILE 4.6 4.4 + - - -
465D GLU* 4.8 6.9 - - - +
475D LYS* 5.5 2.2 - - - +
477D ARG* 3.7 42.4 - - - +
478D GLY* 3.7 6.5 - - - +
554D ASP* 3.0 16.2 + - - +
555D HIS* 2.9 49.4 + - - +
557D SER* 1.3 79.4 + - - +
559D ALA* 1.3 61.6 + - - +
562D GLN* 3.1 13.3 + - + -
563D ARG* 2.9 43.5 + - + +
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Residues in contact with ALA 559 (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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453D ASP* 3.8 18.4 - - + +
454D ALA* 3.8 21.1 - - + +
517D SER* 4.3 0.7 - - - +
521D ALA* 3.6 7.8 - - - +
555D HIS 2.9 16.8 + - - +
556D LEU 3.9 2.0 - - - +
558D ARG* 1.3 77.9 - - - +
560D MET* 1.3 76.9 + - + +
563D ARG* 2.9 35.5 + - - +
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Residues in contact with MET 560 (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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450D PRO* 4.2 13.0 - - + -
517D SER* 3.7 25.8 - - - +
520D ILE* 3.4 30.5 - - + -
521D ALA* 3.8 9.5 - - - -
524D ASN* 3.0 35.7 + - - +
545D ILE* 3.9 17.3 - - + -
556D LEU* 2.9 40.6 + - + +
559D ALA* 1.3 97.2 - - + +
561D TYR* 1.3 75.7 + - + +
564D ILE* 5.6 0.2 - - - +
576D LEU* 5.0 0.2 - - - +
579D PRO* 5.4 0.2 - - + -
581D LEU* 4.3 5.6 - - + -
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Residues in contact with TYR 561 (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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310D ILE* 3.7 24.8 - - - +
311D PRO 5.1 1.6 + - - -
313D GLU* 5.0 4.3 + - - -
557D SER* 3.3 19.9 + - - -
558D ARG 3.8 0.4 - - - -
559D ALA 3.4 1.6 - - - -
560D MET* 1.3 88.7 - - + +
562D GLN* 1.3 97.7 + - + +
563D ARG* 3.1 3.9 + - - -
564D ILE* 3.1 23.1 + - - +
565D SER 3.5 5.5 + - - -
576D LEU* 3.8 30.2 - - + +
577D ASN 3.9 6.7 - - - +
578D LYS* 3.5 52.4 - - + +
579D PRO* 4.0 16.2 + - + -
581D LEU* 4.2 15.5 - - + +
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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