Contacts of the helix formed by residues 582 - 586 (chain B) in PDB entry 5IWM
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 GLY 582 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ASP* 3.4 19.7 - - - -
509B ALA 5.9 0.4 - - - -
580B TYR* 3.2 13.2 - - - +
581B LYS* 1.3 79.8 - - - +
583B LEU* 1.3 67.7 + - - -
584B GLY 3.2 3.1 - - - -
585B GLU* 3.3 16.7 + - - +
586B MET* 4.2 1.0 - - - +
123C PHE* 3.8 15.1 - - - -
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 4.0 5.8 - - + -
438B SER 4.4 0.2 - - - -
439B ALA* 3.6 19.8 - - + +
442B SER* 3.3 14.4 + - - -
443B THR* 4.0 10.3 - - - +
506B MET* 3.9 45.1 - - + +
507B THR 4.9 0.2 - - - +
508B ASP* 3.2 20.8 + - - +
509B ALA* 5.4 1.6 - - + +
542B PRO* 3.9 30.1 - - + -
580B TYR* 6.2 0.7 - - + -
582B GLY* 1.3 69.1 - - - -
584B GLY* 1.3 57.1 + - - +
585B GLU 3.0 5.4 - - - -
586B MET* 3.0 38.3 + - - +
591B LEU* 4.1 14.1 - - + +
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Residues in contact with GLY 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B SER* 3.0 29.8 + - - -
439B ALA* 4.0 1.8 - - - +
442B SER* 3.7 5.6 - - - -
582B GLY* 3.2 2.2 - - - -
583B LEU* 1.3 77.0 - - - +
585B GLU* 1.3 56.9 + - - +
586B MET 3.3 0.2 - - - -
108C GLY* 3.1 2.4 - - - -
109C ASN* 2.7 31.0 + - - +
119C ALA* 4.1 8.1 - - - +
123C PHE* 4.2 10.9 - - - -
124C THR* 4.3 3.3 - - - +
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Residues in contact with GLU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B GLY 4.4 7.3 - - - +
580B TYR* 3.7 21.5 - - + -
581B LYS* 2.7 55.8 + - - +
582B GLY 3.3 13.3 + - - +
583B LEU 3.0 0.4 - - - -
584B GLY* 1.3 77.1 - - - +
586B MET* 1.3 59.2 + - - +
590B GLN* 5.3 0.2 - - - +
66C LYS* 5.0 0.2 - - - -
107C GLN* 3.9 15.6 + - + +
108C GLY* 3.5 12.8 + - - -
123C PHE* 3.2 30.2 - - + +
125C GLU* 3.8 20.0 - - + +
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Residues in contact with MET 586 (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 SER* 3.1 22.4 + - - -
542B PRO* 5.0 0.7 - - - -
543B PRO* 3.9 29.8 - - + +
580B TYR* 3.4 36.8 - - + +
582B GLY 4.2 3.1 - - - +
583B LEU* 3.0 34.0 + - - +
585B GLU* 1.3 79.1 - - - +
587B ASN* 1.3 62.3 + - - +
590B GLN* 3.7 24.0 - - + +
591B LEU* 3.7 34.8 - - + -
594B THR* 4.2 0.7 - - + +
108C GLY* 3.3 11.4 - - - -
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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
------------------------------------------------------------
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