Contacts of the helix formed by residues 584 - 589 (chain A) in PDB entry 4D1Q
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 GLU 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.5 29.5 + - - +
583A THR* 1.3 79.8 - - + +
585A LYS* 1.3 77.0 + - + +
587A ASN* 3.1 20.6 + - - +
13F T 3.4 20.6 - - + +
14F C 3.5 42.0 + - - +
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Residues in contact with LYS 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 5.8 0.6 - - - -
583A THR* 3.3 13.8 - - + +
584A GLU* 1.3 87.4 - - + +
586A ARG* 1.3 59.3 + - + +
587A ASN* 2.7 13.3 + - - -
588A ARG 4.5 0.2 + - - -
580B ASN* 3.1 50.8 + - - +
583B THR* 5.5 1.6 + - - -
4E G 3.3 58.8 + - + +
5E A 3.6 29.5 + - - +
13F T 4.9 9.0 - - + +
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Residues in contact with ARG 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A ASN 4.9 2.2 + - - -
581A ILE* 3.2 36.6 + - - +
583A THR* 3.2 23.2 + - + +
585A LYS* 1.3 76.0 - - + +
587A ASN* 1.3 58.3 + - - -
588A ARG 3.0 3.0 + - - -
589A ILE* 2.9 53.0 + - - +
597A LEU* 4.4 8.5 - - - +
106B CYS* 4.6 8.1 + - - -
107B ARG* 3.0 28.9 + - - +
108B PRO* 3.5 18.1 - - + +
109B PHE* 4.2 12.9 - - - -
5E A 3.7 23.6 - - - +
6E A 2.9 28.1 + - - +
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Residues in contact with ASN 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.8 28.8 - - + +
187A ILE* 3.7 19.9 - - - +
582A ILE* 5.0 4.6 - - - +
583A THR 2.8 9.8 + - - +
584A GLU 3.1 14.2 + - - +
585A LYS 2.7 13.1 + - - -
586A ARG* 1.3 72.7 - - - +
588A ARG* 1.3 79.9 + - - +
589A ILE* 3.2 5.9 + - - +
12F C 3.2 30.7 + - - +
13F T 3.0 30.7 + - - +
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Residues in contact with ARG 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 4.8 16.7 - - - +
585A LYS 4.5 0.8 + - - +
586A ARG 3.0 1.8 + - - -
587A ASN* 1.3 98.7 - - - +
589A ILE* 1.3 66.1 + - - +
590A GLY* 3.3 3.3 + - - -
5E A 4.1 14.6 - - + +
6E A 3.8 29.7 + - - +
7E C 4.0 11.0 - - - +
11F T 3.5 58.0 + - - +
12F C 3.5 19.9 + - - +
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Residues in contact with ILE 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 4.6 8.1 - - - +
189A ARG* 4.7 3.5 + - - -
581A ILE* 3.8 18.8 - - + +
582A ILE* 3.8 32.6 - - + +
586A ARG* 2.9 50.3 + - - +
587A ASN 4.2 5.9 - - - +
588A ARG* 1.3 78.8 - - - +
590A GLY* 1.3 65.1 + - - +
591A GLN 4.1 0.5 + - - -
593A THR* 3.7 24.9 - - + -
594A VAL* 3.4 13.5 - - + +
597A LEU* 3.8 5.6 - - + -
109B PHE* 4.7 2.2 - - + -
6E A 3.4 18.7 - - - +
7E C 4.1 0.4 - - - +
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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