Contacts of the helix formed by residues 598 - 606 (chain D) in PDB entry 5MG3
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 ARG 598 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ARG* 4.5 3.8 - - + -
546D TYR* 3.5 61.3 + - + +
550D PHE* 3.8 15.3 - - + -
594D ILE* 3.3 27.0 + - - +
595D VAL* 3.3 38.1 - - - +
596D GLY 3.3 3.2 - - - -
597D THR* 1.3 76.9 - - - +
599D ALA* 1.4 60.9 + - - +
600D ILE 3.3 0.7 + - - -
601D VAL* 3.3 19.9 + - - +
602D ASN* 3.9 6.6 - - - +
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Residues in contact with ALA 599 (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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2D LEU 3.9 3.7 - - - +
3D ASN* 4.3 2.7 - - - +
4D ARG* 3.5 42.2 - - + +
5D TYR* 4.8 11.1 - - + -
478D ILE* 3.7 22.7 - - + -
596D GLY 5.2 1.3 + - - +
597D THR 3.6 0.8 - - - -
598D ARG* 1.4 73.2 - - - +
600D ILE* 1.3 60.8 + - + +
601D VAL 3.3 0.2 - - - -
602D ASN* 3.3 4.2 + - - +
603D LEU* 2.8 31.6 + - - +
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Residues in contact with ILE 600 (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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478D ILE* 4.0 17.3 - - + +
479D ALA* 3.7 34.3 - - + -
481D SER* 5.7 0.2 - - - +
521D ASN* 4.7 2.2 - - - +
524D ILE* 4.1 13.9 - - + +
525D ASN* 3.5 39.5 - - - +
528D ILE* 4.9 0.2 - - - -
597D THR* 3.4 32.1 - - + +
598D ARG 3.2 0.4 - - - -
599D ALA* 1.3 77.2 - - - +
601D VAL* 1.3 59.5 + - - +
603D LEU* 3.4 10.6 + - + +
604D LEU* 3.1 35.2 + - + +
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Residues in contact with VAL 601 (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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524D ILE* 3.9 19.3 - - + -
528D ILE* 3.8 34.5 - - + +
542D ILE* 4.0 33.2 - - + +
545D GLY* 4.0 11.0 - - - -
546D TYR* 4.6 2.7 - - + -
549D ALA* 4.4 2.0 - - + -
550D PHE* 4.1 18.6 - - + -
598D ARG 3.5 13.5 - - - +
599D ALA 3.3 0.6 - - - -
600D ILE* 1.3 72.4 - - - +
602D ASN* 1.4 64.0 + - - +
605D TYR* 3.2 35.5 + - + +
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Residues in contact with ASN 602 (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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1D MET 4.2 8.7 + - - +
2D LEU* 3.2 39.6 - - + +
4D ARG* 3.0 43.9 + - - +
542D ILE* 3.3 37.1 - - - +
598D ARG 3.9 5.0 - - - +
599D ALA 3.3 3.0 + - - +
601D VAL* 1.4 73.1 - - - +
603D LEU* 1.3 66.2 + - - +
605D TYR* 4.3 0.8 - - - +
606D GLY 3.3 12.6 + - - -
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Residues in contact with LEU 603 (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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2D LEU* 4.3 20.4 + - + +
473D LYS 5.9 3.4 - - - +
475D PHE* 3.9 26.7 - - + +
478D ILE* 3.8 32.3 - - + -
479D ALA* 4.9 10.8 - - + -
525D ASN* 4.9 3.4 - - - +
599D ALA 2.8 21.8 + - - +
600D ILE* 3.4 24.9 - - + +
602D ASN* 1.3 74.0 - - - +
604D LEU* 1.3 76.0 + - + +
606D GLY* 3.9 11.1 + - - +
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Residues in contact with LEU 604 (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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472D TYR* 6.3 4.7 - - + -
473D LYS* 6.4 1.6 - - + -
525D ASN* 3.2 46.0 - - + +
528D ILE* 3.8 18.5 - - + +
529D LYS* 4.6 18.5 - - + +
532D LEU* 3.3 19.8 - - - +
600D ILE* 3.1 25.8 + - + +
601D VAL 3.9 0.2 - - - -
603D LEU* 1.3 91.8 - - + +
605D TYR* 1.3 60.1 + - - +
606D GLY 3.5 5.2 - - - +
612D LYS* 5.0 3.8 - - - +
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Residues in contact with TYR 605 (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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528D ILE* 3.5 27.5 + - + -
531D GLU* 5.4 0.9 - - - +
532D LEU* 3.9 36.8 + - + +
536D ARG* 3.1 23.7 + - - +
537D THR* 2.6 29.6 + - - +
538D VAL* 4.0 14.7 - - + +
541D ALA* 3.7 32.4 + - + -
542D ILE* 4.2 11.7 - - + -
545D GLY* 5.8 0.7 - - - -
601D VAL* 3.2 29.2 + - + +
602D ASN 4.3 1.8 - - - +
604D LEU* 1.3 73.0 - - - +
606D GLY* 1.3 63.8 + - - +
607D GLY 4.3 0.9 - - - +
609D ARG* 4.1 18.5 + - - -
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Residues in contact with GLY 606 (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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2D LEU* 4.4 15.3 - - - -
532D LEU* 5.5 0.3 - - - +
602D ASN 3.3 15.6 + - - -
603D LEU 3.9 8.6 + - - +
604D LEU 3.5 7.0 - - - +
605D TYR* 1.3 78.3 - - - +
607D GLY* 1.3 67.5 + - - +
608D LYS 4.4 3.8 - - - +
609D ARG* 4.8 1.8 - - - -
612D LYS* 4.6 5.9 + - - -
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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