Contacts of the helix formed by residues 623 - 631 (chain A) in PDB entry 1U9J
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 ILE 623 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLU* 5.0 0.2 - - - -
564A ASN 4.2 14.8 - - - +
566A GLY 3.4 22.0 - - - +
568A PRO* 3.6 32.5 - - + -
621A PRO* 3.8 7.5 + - + +
622A SER* 1.3 78.0 + - - +
624A ARG* 1.3 60.7 + - - +
625A ASN 3.2 2.5 - - - +
626A ALA* 3.1 12.7 + - + +
627A HIS* 2.9 56.7 + - + +
632A TRP* 4.3 4.9 - - + -
633A GLU* 5.6 0.2 - - + -
634A PRO* 3.9 21.3 - - + -
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Residues in contact with ARG 624 (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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301A SO4 2.6 45.6 + - - -
445A ASP* 2.9 24.2 + - - -
448A HIS* 3.9 4.9 - - - -
622A SER* 3.6 17.0 + - - +
623A ILE* 1.3 77.2 - - - +
625A ASN* 1.3 63.8 + - - +
627A HIS* 3.0 17.6 + - + +
628A ARG* 2.8 32.0 + - - +
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Residues in contact with ASN 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SO4 4.2 6.6 + - - -
445A ASP* 5.6 0.4 - - - +
446A GLU* 3.5 27.1 + - - +
447A ASP* 2.8 28.5 + - - +
561A GLU* 4.1 7.6 + - - -
562A ILE 2.9 25.5 + - - +
563A ILE* 4.2 9.0 - - + -
622A SER* 5.2 0.2 + - - -
623A ILE* 3.2 1.0 - - - +
624A ARG* 1.3 82.2 + - - +
626A ALA* 1.3 58.8 + - - +
628A ARG* 2.9 27.2 + - - +
629A CYS* 2.8 35.9 + - - +
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Residues in contact with ALA 626 (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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446A GLU* 5.0 0.2 + - - -
563A ILE* 3.8 22.1 - - + +
564A ASN 4.0 10.8 - - - +
565A ILE* 5.6 1.3 - - + -
623A ILE* 3.1 11.1 + - + +
625A ASN* 1.3 75.4 - - - +
627A HIS* 1.3 61.3 + - - +
630A LEU* 2.9 41.0 + - + +
631A ASP 3.2 1.9 + - - -
632A TRP* 3.4 32.1 + - + -
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Residues in contact with HIS 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 2.9 48.7 + - + +
624A ARG* 3.0 21.5 + - + +
626A ALA* 1.3 76.7 - - - +
628A ARG* 1.3 58.2 + - - +
631A ASP* 2.7 33.4 + - - +
632A TRP 3.1 22.3 + - - +
633A GLU* 4.1 23.9 + - + +
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Residues in contact with ARG 628 (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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301A SO4 4.1 16.1 + - - -
447A ASP* 4.7 0.8 + - - -
557A ARG* 2.9 27.2 + - - -
561A GLU* 2.6 41.0 + - - -
624A ARG 2.8 15.7 + - - +
625A ASN* 2.9 39.2 + - - +
627A HIS* 1.3 81.3 - - - +
629A CYS* 1.3 67.1 + - - +
631A ASP* 4.5 1.2 - - - +
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Residues in contact with CYS 629 (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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554A ALA* 5.0 2.4 + - - +
557A ARG* 3.5 53.8 + - - +
558A CYS* 4.1 4.9 - - - -
561A GLU* 3.8 15.9 - - - -
563A ILE* 4.1 8.1 - - + -
625A ASN* 2.8 24.1 + - - +
628A ARG* 1.3 103.7 - - - +
630A LEU* 1.3 76.7 + - + +
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Residues in contact with LEU 630 (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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546A ALA* 3.7 33.2 - - + +
549A ARG* 2.9 35.2 + - + +
550A ILE* 3.9 24.5 - - + +
557A ARG* 5.3 0.9 - - - +
558A CYS* 3.3 34.5 - - - -
563A ILE* 4.3 9.6 - - + -
565A ILE* 5.3 0.2 - - + -
626A ALA* 2.9 27.7 + - + +
629A CYS* 1.3 88.6 - - + +
631A ASP* 1.3 73.5 + - - +
632A TRP* 3.8 7.6 - - + -
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Residues in contact with ASP 631 (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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549A ARG* 2.7 17.8 + - - +
557A ARG* 3.3 34.4 + - - -
627A HIS* 2.7 25.9 + - - +
628A ARG 4.5 0.9 - - - +
630A LEU* 1.3 71.6 - - - +
632A TRP* 1.3 55.4 + - - +
633A GLU* 4.3 0.5 + - - +
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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