Contacts of the strand formed by residues 619 - 624 (chain A) in PDB entry 1HMU
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 MET 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A TYR* 3.8 39.7 - - + -
465A PHE* 3.7 31.0 - - + -
612A VAL 4.0 0.3 - - - +
613A TYR* 3.4 3.3 - - - -
614A HIS* 2.7 37.5 + - + +
617A LEU* 4.0 20.4 - - + +
618A ASP* 1.3 79.6 - - - +
620A VAL* 1.3 66.5 + - - +
621A GLN* 3.8 12.1 - - - -
646A LEU* 3.7 14.8 - - + -
647A ILE 3.3 12.1 - - - +
648A LYS* 4.0 22.7 - - + -
650A ILE* 4.7 0.4 - - - -
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Residues in contact with VAL 620 (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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603A LEU* 4.5 3.1 - - + -
612A VAL 3.4 7.4 - - - +
613A TYR* 3.6 33.0 - - + -
619A MET* 1.3 73.1 - - - +
621A GLN* 1.3 73.0 + - - +
622A ALA* 4.7 3.1 - - + +
630A LEU* 4.4 21.1 - - + -
632A VAL* 4.2 11.7 - - + -
637A ILE* 4.4 12.6 - - + -
645A VAL* 4.0 1.9 - - + +
646A LEU* 3.5 3.6 - - - +
647A ILE* 2.8 43.4 + - + +
650A ILE* 3.8 25.5 - - + +
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Residues in contact with GLN 621 (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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439A VAL* 5.7 0.2 - - + -
444A TYR* 4.3 0.2 - - - +
445A GLY 3.2 23.3 + - - +
446A ALA* 3.4 8.4 - - + +
463A PHE* 3.1 46.8 - - + +
464A PHE 3.0 23.9 + - - -
465A PHE* 3.6 22.3 - - + -
611A ALA* 3.3 2.8 - - - +
612A VAL 2.9 34.4 + - - +
619A MET* 3.8 10.7 - - + -
620A VAL* 1.3 73.3 - - - +
622A ALA* 1.3 61.6 + - - +
645A VAL 3.5 4.7 - - - +
646A LEU* 3.7 22.4 - - + +
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Residues in contact with ALA 622 (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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439A VAL* 5.4 0.2 - - - +
446A ALA* 5.2 0.8 - - - +
463A PHE* 4.4 0.6 - - - -
609A LEU* 4.6 1.1 - - + -
610A GLN 3.6 4.0 - - - -
611A ALA* 3.7 15.9 - - + -
620A VAL* 4.7 2.2 - - + -
621A GLN* 1.3 76.1 - - - +
623A ILE* 1.3 66.6 + - - +
624A PHE* 3.6 26.4 + - + -
630A LEU* 4.0 10.5 - - + -
643A CYS 4.1 0.3 - - - +
644A ALA* 3.3 3.5 - - - -
645A VAL* 2.8 47.5 + - + +
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Residues in contact with ILE 623 (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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435A PHE* 3.9 16.2 - - + -
438A GLY* 5.5 0.2 - - - -
446A ALA* 4.3 21.5 - - + +
447A SER 4.3 2.5 - - - +
448A ALA* 3.5 35.0 - - + +
461A ALA* 4.3 4.5 - - + -
463A PHE* 4.0 17.0 - - + -
609A LEU* 3.4 6.9 - - - +
610A GLN* 2.8 38.6 + - + +
622A ALA* 1.3 81.2 - - - +
624A PHE* 1.3 61.8 + - - +
625A TYR* 3.6 22.9 + - + -
643A CYS 3.8 2.0 - - - +
644A ALA* 3.7 20.9 - - + -
661A PRO* 5.8 0.2 - - + -
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Residues in contact with PHE 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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435A PHE* 3.9 4.5 - - - -
608A GLN 3.9 3.8 - - - -
609A LEU* 3.6 24.0 - - + -
622A ALA* 3.6 25.6 - - + -
623A ILE* 1.3 73.7 - - - +
625A TYR* 1.3 63.4 + - - +
626A THR 3.5 13.9 - - - +
628A GLY* 3.7 28.0 - - - -
629A LYS 4.2 9.4 - - - -
630A LEU* 4.2 13.7 - - + -
637A ILE* 4.5 17.0 - - + -
639A THR* 3.6 26.2 - - + -
642A PRO* 3.2 3.0 - - + +
643A CYS* 2.8 51.0 + - - +
645A VAL* 3.9 15.7 - - + -
670A LEU* 5.4 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