Contacts of the helix formed by residues 442 - 453 (chain B) in PDB entry 5M5X
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 ASP 442 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B LEU* 5.2 1.5 - - - +
438B ILE* 5.1 10.1 - - + +
439B ASN* 4.1 16.3 + - - +
440B PHE* 3.1 10.0 - - - +
441B LYS* 1.3 80.4 - - - +
443B LYS* 1.3 81.7 + - - +
444B ARG* 3.1 26.6 + - - +
445B TYR* 4.5 8.7 + - + +
446B MET* 3.7 16.5 + - - +
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Residues in contact with LYS 443 (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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152B LEU* 3.6 37.9 - - + +
153B PHE 3.8 20.6 + - - -
154B GLU* 4.3 17.7 - - - +
441B LYS 5.4 1.6 - - - +
442B ASP* 1.3 81.0 + - - +
444B ARG* 1.3 61.5 + - - +
446B MET* 3.4 15.5 + - + +
447B SER* 3.0 28.9 + - - +
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Residues in contact with ARG 444 (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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442B ASP* 3.1 19.2 + - - +
443B LYS* 1.3 77.6 - - - +
445B TYR* 1.3 59.6 + - - +
447B SER* 3.0 22.8 + - - +
448B ARG* 3.1 17.2 + - + +
4S A 4.6 2.2 - - - -
5S G 3.2 57.5 - - - +
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Residues in contact with TYR 445 (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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428B VAL* 6.0 0.7 - - - -
431B ASP* 2.5 36.4 + - - +
436B MET 5.2 2.5 - - - -
437B ALA* 4.6 2.3 - - - +
438B ILE* 3.6 44.6 - - + -
439B ASN 4.5 5.6 - - - +
440B PHE* 3.4 43.4 - + - -
442B ASP* 4.1 9.7 + - + +
443B LYS 3.5 0.2 - - - -
444B ARG* 1.3 79.1 - - - +
446B MET* 1.3 62.3 + - - +
448B ARG* 3.1 39.5 + - - +
449B VAL* 3.0 40.8 + - + +
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Residues in contact with MET 446 (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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141B LEU* 6.6 0.2 - - - -
143B TRP* 3.5 58.3 - - + +
152B LEU* 6.1 3.6 - - + -
154B GLU* 5.9 6.5 - - + -
440B PHE* 4.7 17.5 - - + +
442B ASP 3.7 13.7 + - - +
443B LYS* 3.4 24.8 + - + +
444B ARG 3.2 0.2 - - - -
445B TYR* 1.3 80.5 - - - +
447B SER* 1.3 56.9 + - - +
448B ARG 3.1 0.2 - - - -
449B VAL* 4.3 8.5 - - + -
450B LEU* 3.1 51.5 + - + +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 6.1 1.2 - - - +
443B LYS* 3.0 16.0 + - - +
444B ARG* 3.0 13.7 + - - -
446B MET* 1.3 75.6 - - - +
448B ARG* 1.3 58.2 + - - +
450B LEU* 5.2 1.6 - - - -
451B MET* 3.2 24.2 - - - +
6S T 3.2 21.3 + - - -
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Residues in contact with ARG 448 (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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444B ARG 3.2 16.6 - - - +
445B TYR* 3.1 45.8 + - - +
447B SER* 1.3 80.7 - - - +
449B VAL* 1.3 64.9 + - - +
450B LEU 3.3 1.1 - - - -
451B MET* 4.0 5.9 - - - +
452B ARG* 3.4 25.5 + - - +
5S G 2.8 51.7 + - + +
6S T 4.4 24.4 - - + +
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Residues in contact with VAL 449 (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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424B ILE* 5.0 2.1 - - + +
427B GLN* 3.7 30.1 - - + +
428B VAL* 4.0 26.9 - - + -
431B ASP* 6.1 1.6 - - + -
440B PHE* 5.0 2.7 - - + -
445B TYR* 3.0 42.4 + - + +
446B MET* 4.0 17.0 - - + +
448B ARG* 1.3 76.6 - - - +
450B LEU* 1.3 61.7 + - + +
452B ARG* 4.1 7.1 + - - +
453B VAL* 3.3 24.4 + - - +
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Residues in contact with LEU 450 (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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141B LEU* 5.0 15.9 - - + -
154B GLU* 4.9 4.7 - - - +
156B ARG* 3.2 42.7 + - - +
424B ILE* 3.7 29.2 - - + -
446B MET* 3.1 33.8 + - + +
447B SER* 5.2 1.6 - - - -
449B VAL* 1.3 78.6 - - + +
451B MET* 1.3 61.3 + - - +
453B VAL* 3.2 18.9 - - - +
455B GLU* 3.4 25.7 - - - +
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Residues in contact with MET 451 (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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156B ARG* 5.3 8.2 + - - +
447B SER* 3.2 20.9 + - - +
448B ARG* 3.7 8.5 + - - +
449B VAL 3.4 0.4 - - - -
450B LEU* 1.3 79.8 - - - +
452B ARG* 1.3 73.4 + - + +
453B VAL 3.2 9.8 - - - +
6S T 3.8 54.5 - - + +
7S A 3.8 30.3 - - - +
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Residues in contact with ARG 452 (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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427B GLN* 2.7 36.5 + - - +
430B MET* 4.3 5.1 - - - +
431B ASP* 6.2 0.4 - - - +
448B ARG 3.4 15.9 + - - +
449B VAL* 4.1 8.3 + - - +
450B LEU 3.5 0.2 - - - -
451B MET* 1.3 85.3 - - + +
453B VAL* 1.3 65.7 + - + +
454B ASN 3.8 0.2 + - - -
7S A 5.4 8.1 - - - +
8S C 6.3 1.3 - - - +
29T T 4.1 14.0 - - - +
30T A 3.1 62.5 + - - +
31T G 5.1 7.2 - - - -
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TYR* 5.4 0.7 - - + +
423B ASN* 3.7 17.5 - - - +
424B ILE* 3.7 21.8 - - + -
427B GLN* 3.9 25.6 - - + +
449B VAL 3.3 18.2 - - - +
450B LEU 3.2 20.4 - - - +
451B MET 3.2 10.0 - - - +
452B ARG* 1.3 82.8 - - + +
454B ASN* 1.3 60.4 + - - +
455B GLU* 3.2 32.4 + - + +
29T T 5.2 3.4 - - - +
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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