Contacts of the helix formed by residues 506 - 511 (chain C) in PDB entry 3IW4
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 ALA 506 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504C TYR 3.5 1.2 + - - -
505C ILE* 1.3 81.9 - - - +
507C PRO* 1.3 72.3 - - + +
508C GLU* 3.3 30.5 - - + +
509C ILE* 3.4 6.3 + - + +
510C ILE* 3.4 18.2 + - - +
519C VAL* 3.6 18.9 - - + +
522C TRP* 3.3 25.1 - - + -
580C ARG* 4.2 0.2 - - - +
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Residues in contact with PRO 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ALA* 1.3 89.4 - - + +
508C GLU* 1.3 65.7 + - - +
510C ILE 3.2 2.4 + - - -
511C ALA* 3.0 21.2 + - - +
522C TRP* 3.4 33.0 - - + -
550C ILE* 4.2 7.9 - - + -
551C MET* 3.5 30.4 - - + +
575C LYS* 3.6 47.6 - - + +
580C ARG* 4.1 0.2 - - - +
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Residues in contact with GLU 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ALA* 3.3 9.8 - - - +
507C PRO* 1.3 76.7 - - - +
509C ILE* 1.3 63.3 + - - +
511C ALA* 3.4 1.5 + - - -
512C TYR 3.4 1.9 + - - -
513C GLN* 3.0 52.3 + - + +
514C PRO 5.3 0.9 - - - +
515C TYR* 3.7 22.7 - - + -
518C SER* 2.9 14.1 + - - +
519C VAL* 3.2 7.9 - - + +
575C LYS 5.0 0.2 + - - -
577C PRO* 3.5 23.8 - - + +
580C ARG* 2.6 49.3 + - - -
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Residues in contact with ILE 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C ARG* 5.8 2.0 - - + -
496C ARG 5.3 0.7 - - - +
498C PHE* 3.8 39.1 - - + +
499C CYS* 4.2 18.8 - - - +
505C ILE* 3.6 27.1 - - + -
506C ALA* 3.4 6.6 + - + +
507C PRO 3.3 0.8 - - - -
508C GLU* 1.3 76.4 - - - +
510C ILE* 1.3 58.1 + - - +
512C TYR* 3.0 22.5 + - - +
515C TYR* 3.8 26.0 - - + +
519C VAL* 3.6 39.0 - - + -
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Residues in contact with ILE 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498C PHE* 5.3 5.8 - - + -
505C ILE* 3.7 16.4 - - + +
506C ALA 3.5 17.3 - - - +
507C PRO 3.2 5.3 + - - +
509C ILE* 1.3 76.8 - - - +
511C ALA* 1.3 58.9 + - - +
512C TYR* 3.1 16.5 + - - -
547C PHE* 3.6 55.4 - - + +
550C ILE* 3.5 31.4 - - + -
551C MET* 3.8 18.4 - - + -
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Residues in contact with ALA 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C PRO 3.0 14.3 + - - +
508C GLU* 4.6 0.4 - - - -
509C ILE 3.2 0.4 - - - -
510C ILE* 1.3 75.8 - - - +
512C TYR* 1.3 70.6 + - - +
513C GLN* 2.7 32.2 + - + +
551C MET* 4.8 12.3 - - + -
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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