Contacts of the strand formed by residues 601 - 605 (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 LYS 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A ALA 3.5 3.7 + - - +
600A PRO* 1.3 71.9 - - - +
602A VAL* 1.3 74.1 + - - +
603A LEU* 3.2 26.3 + - + +
612A VAL* 3.4 3.2 - - - -
613A TYR* 2.8 66.4 + - + +
615A GLN* 6.6 0.2 - - + -
632A VAL* 5.0 3.2 - - - +
633A ALA 5.5 2.6 - - - +
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Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A VAL* 4.5 11.2 - - + -
472A LEU* 3.8 35.0 - - + -
530A PRO* 5.0 15.9 - - + -
531A GLU* 5.5 8.5 - - - +
579A ALA* 4.8 8.1 - - + -
581A ILE* 5.9 0.9 - - + -
600A PRO 3.9 4.0 + - - +
601A LYS* 1.3 79.3 - - - +
603A LEU* 1.3 62.9 + - - +
604A ALA* 3.8 24.0 - - - +
605A ASN* 4.1 8.3 - - + +
611A ALA 3.7 4.0 - - - -
612A VAL* 4.5 1.8 - - + -
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Residues in contact with LEU 603 (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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601A LYS* 3.2 34.5 + - + +
602A VAL* 1.3 74.4 - - - +
604A ALA* 1.3 63.7 + - - +
611A ALA* 2.8 12.9 + - + +
612A VAL 4.1 6.1 - - - +
613A TYR* 3.6 32.5 - - + +
620A VAL* 4.5 4.0 - - + -
630A LEU* 3.7 34.7 - - + +
631A SER 4.4 5.2 - - - +
632A VAL* 3.8 29.6 - - + -
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Residues in contact with ALA 604 (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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472A LEU* 3.9 1.2 - - - +
602A VAL* 3.5 7.0 - - - +
603A LEU* 1.3 83.6 - - + +
605A ASN* 1.3 64.2 + - - +
606A THR* 5.2 5.4 - - + -
609A LEU* 3.6 37.9 - - + +
610A GLN* 3.2 1.4 - - - -
611A ALA 2.9 27.2 + - - +
630A LEU* 4.8 3.1 - - + -
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Residues in contact with ASN 605 (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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472A LEU* 3.9 13.7 - - + +
473A GLY 3.1 19.3 + - - +
474A ALA* 3.3 8.0 - - - +
531A GLU* 5.9 1.3 + - - +
577A GLN* 4.0 28.7 + - - +
578A TYR 3.1 17.4 + - - -
579A ALA* 4.6 3.0 - - - +
602A VAL* 4.1 13.4 - - + +
604A ALA* 1.3 77.3 - - - +
606A THR* 1.3 65.9 + - - +
609A LEU 3.5 1.8 - - - -
610A GLN* 2.7 34.1 + - - +
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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