Contacts of the helix formed by residues 528 - 534 (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 MET 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482B ILE* 3.8 33.9 - - + -
485B PHE* 3.7 37.2 - - + -
487B THR* 4.0 12.8 - - - +
488B GLY 4.1 2.0 - - - +
489B ILE* 3.9 11.0 - - + -
493B PHE* 3.8 24.2 - - + -
523B PHE* 4.1 10.5 - - + -
524B PHE* 2.8 34.1 + - - +
527B PHE* 1.3 81.1 - - + +
529B ARG* 1.3 58.6 + - - +
530B PRO* 3.3 5.2 - - - -
531B LEU* 2.9 37.0 + - + +
532B ILE* 3.7 3.8 + - - +
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Residues in contact with ARG 529 (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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524B PHE 3.0 6.7 + - - -
525B TYR* 3.2 49.8 + - + +
526B ARG 5.7 0.2 - - - -
527B PHE 3.7 1.2 - - - -
528B MET* 1.3 75.8 - - - +
530B PRO* 1.4 69.5 - - + +
532B ILE* 3.1 16.8 + - + +
533B GLU* 3.0 35.2 + - + +
608B LEU* 4.1 8.3 - - + +
611B ALA* 3.4 30.5 - - - +
615B ASP* 4.5 10.1 + - - -
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Residues in contact with PRO 530 (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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490B GLY 5.7 1.8 - - - +
493B PHE* 3.5 35.7 - - + -
495B LEU* 4.4 7.2 - - + +
527B PHE 5.3 0.7 - - - +
528B MET* 3.3 6.5 - - - -
529B ARG* 1.4 95.6 - - + +
531B LEU* 1.3 59.8 + - - +
533B GLU* 3.3 18.6 + - - +
534B ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 531 (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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485B PHE* 4.5 9.0 - - + -
487B THR* 4.7 9.6 - - + -
493B PHE* 3.6 23.1 - - + -
495B LEU* 4.3 7.6 - - + -
498B ALA* 4.9 2.2 - - + -
503B ILE* 4.3 21.3 - - + -
524B PHE* 4.8 3.8 - - + -
528B MET* 2.9 40.4 + - + +
530B PRO* 1.3 80.1 - - - +
532B ILE* 1.3 57.9 + - - +
534B ALA* 3.7 1.2 + - - +
535B GLY 3.7 1.7 + - - -
536B TYR* 3.1 63.5 + - + +
537B VAL* 4.0 18.4 - - + -
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Residues in contact with ILE 532 (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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14A ILE* 3.8 25.8 - - + -
521B LEU* 4.8 3.1 - - + +
524B PHE* 4.0 10.5 - - + +
525B TYR* 3.9 34.5 - - + +
528B MET 4.2 5.2 - - - +
529B ARG* 3.1 9.5 + - + +
531B LEU* 1.3 73.5 - - - +
533B GLU* 1.3 55.9 + - + +
534B ALA 3.1 2.2 - - - -
535B GLY* 2.7 26.5 + - - -
536B TYR 4.8 0.2 - - - +
537B VAL* 4.0 22.9 - - + +
606B VAL* 3.9 38.3 - - + +
607B LYS* 5.0 0.4 - - - +
608B LEU* 4.7 18.4 + - + -
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Residues in contact with GLU 533 (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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529B ARG* 3.0 47.2 + - - +
530B PRO* 3.3 18.8 + - - +
532B ILE* 1.3 76.7 - - - +
534B ALA* 1.3 58.9 + - - +
535B GLY 3.2 1.0 + - - -
607B LYS* 6.0 0.3 + - - -
608B LEU* 3.7 27.0 - - + +
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Residues in contact with ALA 534 (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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495B LEU* 3.9 21.5 - - + -
530B PRO 3.0 15.6 + - - +
531B LEU 4.0 2.5 - - - +
532B ILE 3.1 0.4 - - - -
533B GLU* 1.3 76.2 - - - +
535B GLY* 1.3 61.0 + - - +
536B TYR* 3.4 33.2 - - + -
605B GLN* 4.8 0.7 - - - +
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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