Contacts of the helix formed by residues 597 - 602 (chain F) in PDB entry 1AM4
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 TRP 597 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509F VAL* 3.4 22.7 - - + -
510F GLY* 3.3 35.2 - - - -
511F ASP* 2.9 26.5 + - + +
560F GLY 3.7 7.0 - - - -
568F ARG* 3.1 31.2 - - - -
580F VAL* 3.8 19.1 - - + -
581F CYS 4.9 2.0 - - - -
589F SER 5.6 0.4 - - - -
592F ASN* 2.8 31.6 + - + -
593F VAL* 3.6 10.1 - - - +
596F LYS* 1.3 102.5 - - + +
598F VAL* 1.3 73.2 + - - +
600F GLU* 3.1 34.3 - - + +
601F ILE* 3.0 27.8 + - + +
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Residues in contact with VAL 598 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580F VAL* 4.9 12.3 - - + -
593F VAL* 2.8 26.6 + - + +
594F LYS* 4.4 2.9 - - - +
597F TRP* 1.3 67.7 - - - +
599F PRO* 1.3 67.9 - - + +
601F ILE* 2.6 39.2 + - + +
602F THR* 2.9 24.9 + - - +
610F PHE* 5.5 9.9 - - + -
649F LEU* 3.7 49.6 - - + +
651F ALA* 6.4 1.1 - - + -
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Residues in contact with PRO 599 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594F LYS 2.9 30.1 - - - +
595F GLU* 5.1 0.4 - - - -
596F LYS* 3.9 10.3 - - - +
597F TRP 3.5 2.0 - - - -
598F VAL* 1.3 98.3 - - + +
600F GLU* 1.3 53.0 + - - +
601F ILE 3.0 0.2 + - - -
602F THR* 4.3 5.4 - - - +
603F HIS* 2.5 42.7 + - + +
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Residues in contact with GLU 600 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565F ASP* 3.6 23.0 - - - +
568F ARG* 2.6 34.2 + - - +
569F PRO* 5.5 3.8 - - + -
572F TYR* 2.8 23.6 + - - +
596F LYS* 3.0 25.4 + - - +
597F TRP* 3.1 21.7 - - + +
599F PRO* 1.3 69.9 - - - +
601F ILE* 1.3 57.4 - - + +
603F HIS* 4.3 6.5 - - - +
604F HIS* 3.2 35.0 - - + +
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Residues in contact with ILE 601 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F VAL* 3.6 30.7 - - + -
572F TYR* 4.9 6.7 - - + +
578F PHE* 3.8 35.5 - - + -
579F LEU 5.7 0.7 - - - +
580F VAL* 4.0 20.9 - - + -
597F TRP* 3.0 12.1 + - + +
598F VAL* 2.6 25.9 + - - +
600F GLU* 1.3 74.9 - - - +
602F THR* 1.3 56.4 + - - +
603F HIS 3.5 0.2 - - - -
604F HIS* 3.9 6.3 - - - -
605F CYS* 3.3 27.6 + - - +
610F PHE* 3.1 37.0 - - + -
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Residues in contact with THR 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598F VAL* 2.9 31.1 + - - +
599F PRO* 4.0 5.2 - - - -
601F ILE* 1.3 74.3 - - - +
603F HIS* 1.3 60.9 - - - +
604F HIS 3.0 6.6 + - - -
605F CYS 4.3 1.6 - - - +
606F PRO* 3.8 29.3 - - + +
607F LYS* 5.7 4.7 - - - +
610F PHE* 4.1 18.9 - - + -
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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