Contacts of the helix formed by residues 563 - 572 (chain A) in PDB entry 4RM9
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 ASP 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 6.2 0.9 - - - -
518A ILE* 6.0 0.5 - - - -
519A THR* 3.8 28.3 + - + +
522A GLU* 4.5 8.3 - - - +
558A MET* 5.8 1.8 - - - -
561A GLY 4.0 0.6 + - - -
562A ARG* 1.3 74.9 - - - +
564A LYS* 1.3 65.1 + - - +
565A TYR* 2.9 9.9 + - - +
566A LYS* 2.9 49.4 + - - +
567A THR* 3.0 24.0 + - - -
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Residues in contact with LYS 564 (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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196A GLN 3.6 16.4 - - - +
197A ASP* 3.3 30.1 + - + +
198A LEU 3.2 19.6 + - - +
199A GLU* 3.2 29.2 + - + +
201A TYR* 4.0 14.9 + - - -
203A ILE* 4.0 8.9 - - - +
221A ASP* 4.7 4.0 + - - -
223A LEU* 4.7 15.7 - - - -
226A ASN* 6.0 0.4 - - - +
519A THR* 5.3 0.6 - - + +
563A ASP* 1.3 75.6 - - - +
565A TYR* 1.3 83.7 + - + +
567A THR* 3.6 5.3 + - - +
568A LEU* 3.1 33.4 + - + +
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Residues in contact with TYR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLN* 3.6 13.0 + - - +
197A ASP* 2.6 34.6 + - + -
223A LEU* 4.8 6.1 - - + -
517A ARG* 3.2 74.7 + - + +
518A ILE* 3.9 5.2 - - - -
519A THR* 3.9 28.7 - - + -
563A ASP* 2.9 4.5 + - - +
564A LYS* 1.3 98.5 - - + +
566A LYS* 1.3 66.1 + - - +
567A THR 3.2 1.1 - - - -
568A LEU* 3.4 14.1 + - + +
569A ARG* 3.0 36.0 + - - +
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Residues in contact with LYS 566 (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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522A GLU* 4.2 16.7 + - - -
561A GLY 3.5 25.8 + - - +
562A ARG* 4.8 4.9 - - + -
563A ASP* 2.9 38.3 + - - +
565A TYR* 1.3 76.0 - - - +
567A THR* 1.3 58.5 + - - +
569A ARG* 3.3 25.3 + - - +
570A GLN* 2.9 29.3 + - - +
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Residues in contact with THR 567 (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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235A THR* 4.2 6.8 - - + +
236A PRO* 4.0 40.4 - - + +
562A ARG* 3.0 46.9 + - - +
563A ASP 3.0 19.0 + - - -
564A LYS* 3.7 5.8 - - - +
566A LYS* 1.3 77.3 - - - +
568A LEU* 1.3 58.2 + - - +
570A GLN* 3.1 2.3 + - - +
571A ILE* 2.9 29.2 + - + +
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Residues in contact with LEU 568 (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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221A ASP* 5.7 0.9 - - - +
223A LEU* 3.6 31.4 - - + -
226A ASN* 3.7 33.0 - - - +
236A PRO* 4.8 4.9 - - + -
564A LYS* 3.1 32.1 + - + +
565A TYR* 3.7 18.4 - - + +
566A LYS 3.4 0.2 - - - -
567A THR* 1.3 76.7 - - - +
569A ARG* 1.3 61.3 + - + +
571A ILE* 3.3 13.2 - - + +
572A ARG* 3.0 58.0 + - - +
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Residues in contact with ARG 569 (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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516A LYS* 3.5 45.5 - - - +
517A ARG 3.4 28.9 + - - +
518A ILE* 5.9 1.2 - - - +
565A TYR* 3.0 25.6 + - - +
566A LYS* 3.5 36.4 - - - +
568A LEU* 1.3 76.5 - - + +
570A GLN* 1.3 66.2 + - - +
572A ARG* 3.3 14.8 + - - +
573A GLN* 3.4 19.2 + - - +
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Residues in contact with GLN 570 (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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562A ARG* 4.1 23.9 - - - +
566A LYS 2.9 15.1 + - - +
567A THR* 3.4 11.4 - - - +
569A ARG* 1.3 76.1 - - - +
571A ILE* 1.3 62.8 + - + +
573A GLN* 3.2 32.8 + - - +
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Residues in contact with ILE 571 (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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226A ASN* 4.0 1.3 - - - +
236A PRO* 3.2 54.5 - - + +
237A LYS* 3.5 21.9 - - - +
238A ILE* 3.7 3.5 - - - -
239A GLY* 3.1 37.4 + - - +
562A ARG* 5.2 2.2 - - - +
567A THR* 2.9 24.3 + - + +
568A LEU* 3.3 31.4 - - + +
570A GLN* 1.3 74.6 - - + +
572A ARG* 1.3 56.9 + - + +
573A GLN 3.3 2.1 + - - +
579A ARG* 3.3 14.7 - - - +
582A GLU* 5.1 2.0 - - - +
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Residues in contact with ARG 572 (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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223A LEU* 3.4 42.4 + - - +
224A GLY* 4.1 3.6 - - - +
226A ASN* 4.9 3.2 + - - -
239A GLY* 3.7 24.2 - - - +
240A PHE 4.6 2.2 + - - +
241A PRO* 3.7 40.1 - - + +
244A GLU* 5.0 2.1 - - - +
568A LEU* 3.0 50.5 + - - +
569A ARG* 3.3 7.8 + - - +
570A GLN 3.2 1.2 - - - -
571A ILE* 1.3 79.8 - - + +
573A GLN* 1.3 64.0 - - - +
574A GLY 3.8 1.2 + - - +
579A ARG* 3.4 16.1 + - - +
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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