Contacts of the helix formed by residues 567 - 576 (chain A) in PDB entry 1MUK
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 VAL 567 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A TYR* 4.1 30.3 - - + -
308A PHE* 4.9 1.6 - - + -
557A PRO* 4.7 19.5 - - + -
559A SER* 5.9 0.7 - - - -
564A ILE 5.1 1.4 + - - -
565A GLU 3.4 8.2 - - - +
566A LYS* 1.3 79.1 - - - +
568A ILE* 1.3 65.2 + - - +
569A PRO* 3.2 8.3 - - + -
570A LEU* 3.1 38.9 + - + +
571A GLY 3.8 1.7 + - - -
781A TYR* 5.7 2.3 - - + -
782A LEU* 5.0 4.9 - - + -
786A PHE* 5.2 0.5 - - - -
1101A SER* 4.1 27.5 - - - +
1102A THR 5.8 0.8 - - - +
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Residues in contact with ILE 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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563A VAL* 3.6 39.7 - - + +
564A ILE* 5.3 2.9 - - - +
566A LYS 3.2 2.6 + - - -
567A VAL* 1.3 73.1 - - - +
569A PRO* 1.3 69.8 - - + +
571A GLY 3.1 11.6 + - - -
572A VAL* 3.2 18.8 + - + +
784A LEU* 3.9 12.6 - - + -
786A PHE* 3.6 24.6 - - + -
791A ARG* 4.1 20.6 - - + +
1077A LEU 6.1 0.2 - - - +
1098A MET 5.6 1.1 - - - +
1186A SER* 4.7 21.8 - - - -
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Residues in contact with PRO 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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297A LEU* 4.2 4.5 - - + +
306A TYR 4.8 0.4 - - - +
308A PHE* 3.4 30.5 - - + -
567A VAL* 3.2 9.4 - - + -
568A ILE* 1.3 96.9 - - + +
570A LEU* 1.3 61.6 + - - +
572A VAL* 3.2 13.4 + - + +
573A TYR* 3.1 22.2 + - - +
1098A MET* 3.2 26.9 - - + +
1099A LEU* 3.5 21.1 - - + +
1100A GLN* 3.7 10.5 - - - +
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Residues in contact with LEU 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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299A TRP* 3.5 33.4 - - + -
306A TYR* 3.9 11.9 - - + -
308A PHE* 3.6 18.2 - - + -
567A VAL* 3.1 23.9 + - + +
569A PRO* 1.3 77.9 - - - +
571A GLY* 1.3 59.7 + - - +
573A TYR* 3.1 5.2 + - + +
574A ALA* 2.8 30.5 + - - +
730A VAL* 3.6 36.6 - - + -
737A LEU* 4.4 5.4 - - + -
739A ILE* 3.5 18.4 - - + -
781A TYR* 4.1 16.2 - - + -
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Residues in contact with GLY 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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567A VAL 3.8 2.8 + - - -
568A ILE 3.1 6.4 + - - -
570A LEU* 1.3 78.8 - - - +
572A VAL* 1.3 56.1 + - - +
574A ALA* 3.8 5.9 - - - +
575A SER* 2.9 35.5 + - - -
737A LEU* 5.2 4.9 - - - +
779A ALA* 4.6 2.6 - - - +
781A TYR* 6.2 2.0 - - - -
786A PHE* 3.6 33.4 - - - +
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Residues in contact with VAL 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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295A PRO* 3.9 18.4 - - + -
297A LEU* 3.9 19.3 - - + -
568A ILE* 3.2 29.1 + - + +
569A PRO* 3.2 13.4 + - + +
571A GLY* 1.3 76.2 - - - +
573A TYR* 1.3 58.7 + - - +
575A SER* 4.0 4.5 - - - -
576A SER* 2.7 33.1 + - - -
786A PHE* 3.9 5.8 - - + -
789A GLY* 3.1 28.4 - - - +
791A ARG* 5.9 0.7 - - + +
1077A LEU* 4.7 11.7 - - + +
1099A LEU* 5.8 4.0 - - + -
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Residues in contact with TYR 573 (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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297A LEU* 3.6 37.4 - - + +
298A GLU* 4.6 0.4 - - - -
299A TRP* 3.6 39.6 - + + +
303A ARG* 3.5 7.8 + - - -
308A PHE* 3.6 31.0 - + + -
569A PRO 3.1 3.0 + - - +
570A LEU 3.4 8.1 - - - +
572A VAL* 1.3 80.7 - - - +
574A ALA* 1.3 67.0 + - - +
576A SER* 3.3 11.5 + - - -
579A ASN* 3.0 43.1 + - - +
739A ILE* 4.0 9.4 - - + -
741A ASP* 2.9 38.8 + - - -
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Residues in contact with ALA 574 (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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570A LEU 2.8 19.4 + - - +
571A GLY* 4.0 4.0 - - - +
573A TYR* 1.3 73.2 - - - +
575A SER* 1.3 59.0 + - - +
576A SER 3.4 0.4 + - - -
579A ASN* 4.6 0.9 - - - -
580A GLN* 3.6 30.0 + - - -
581A SER* 3.7 16.5 + - - +
737A LEU* 4.1 9.2 - - + -
739A ILE* 3.9 41.7 - - + -
779A ALA* 4.8 1.6 - - + -
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Residues in contact with SER 575 (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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571A GLY 2.9 21.2 + - - -
574A ALA* 1.3 78.0 - - - +
576A SER* 1.3 61.6 + - - +
577A PRO* 3.5 3.5 - - - +
579A ASN 4.6 3.2 - - - +
581A SER* 4.8 0.7 - - - -
777A GLY 5.3 3.3 - - - +
778A THR* 5.4 1.3 - - - -
779A ALA* 4.0 9.2 - - - -
786A PHE* 3.5 32.7 - - - +
787A ILE* 4.3 0.2 - - - -
788A PHE* 3.1 22.8 + - - -
789A GLY* 2.6 30.0 + - - -
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Residues in contact with SER 576 (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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294A CYS* 4.3 0.9 - - - -
295A PRO* 3.5 32.3 + - - +
296A ASN* 5.7 0.4 - - - -
297A LEU* 5.8 2.4 - - - +
572A VAL 2.7 22.2 + - - -
573A TYR* 3.3 9.1 + - - -
574A ALA 3.4 0.2 - - - -
575A SER* 1.3 76.3 - - - +
577A PRO* 1.3 74.4 - - - +
578A PRO* 4.3 0.3 - - - +
579A ASN* 2.7 28.1 + - - +
789A GLY* 3.2 14.4 - - - +
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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