Contacts of the strand formed by residues 638 - 642 (chain A) in PDB entry 4YZ9
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 GLN 638 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A ARG* 3.4 5.4 - - - -
601A ILE* 2.9 42.7 + - + +
606A PHE* 3.7 33.3 - - + +
609A ALA* 3.7 15.5 - - - +
610A ASP* 2.8 32.5 + - - +
631A THR* 4.6 6.6 + - - +
632A GLU 3.5 8.7 - - - +
633A LYS* 3.7 31.2 - - + +
637A PHE* 1.3 79.8 - - - +
639A TYR* 1.3 67.3 + - - +
640A ILE* 4.2 7.3 - - + +
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Residues in contact with TYR 639 (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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564A VAL* 5.5 1.2 - - - +
566A VAL* 3.7 32.5 - - + +
569A ILE* 3.3 15.1 - - + +
571A PHE* 3.6 36.4 - + - -
587A TYR* 6.3 0.2 - + - -
598A VAL* 4.2 14.1 - - + -
599A LYS 3.3 5.6 - - - +
600A ARG* 3.9 21.3 - - + -
631A THR* 3.1 4.3 + - - -
632A GLU* 2.7 46.8 + - + +
634A ASP* 3.3 33.3 + - - -
636A GLN* 4.7 2.1 + - - -
637A PHE* 3.2 29.1 - - + -
638A GLN* 1.3 78.0 - - - +
640A ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 640 (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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597A ALA 3.7 0.3 - - - +
598A VAL* 3.3 4.3 - - - +
599A LYS* 2.7 46.9 + - - +
601A ILE* 3.9 27.6 - - + -
609A ALA* 4.6 1.6 - - + -
613A VAL* 3.9 24.2 - - + -
628A TYR* 3.7 28.0 - - + -
630A CYS 3.5 2.5 - - - -
631A THR* 3.9 15.3 - - - +
638A GLN* 4.3 9.6 - - - +
639A TYR* 1.3 77.0 - - - +
641A ALA* 1.3 62.4 + - - +
642A ILE* 3.8 17.3 + - + -
1001A 4K7 4.0 17.9 - - + +
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Residues in contact with ALA 641 (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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569A ILE* 4.0 17.5 - - + +
591A PHE* 4.1 14.8 - - + -
596A VAL* 3.9 21.8 - - + -
597A ALA 3.4 5.2 - - - -
598A VAL* 4.4 3.8 - - + +
629A PHE* 3.0 35.3 + - + -
630A CYS 2.9 15.1 + - - +
640A ILE* 1.3 72.6 - - - +
642A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 642 (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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596A VAL* 3.4 6.2 - - - +
597A ALA* 2.7 46.9 + - + +
599A LYS* 3.9 32.5 - - + +
626A ILE* 4.6 7.0 - - + -
627A ARG 3.4 12.1 - - - +
628A TYR* 4.8 0.9 - - - -
629A PHE* 3.8 5.6 - - - -
640A ILE* 4.0 9.2 - - + -
641A ALA* 1.3 79.9 - - - +
643A GLU* 1.3 68.6 + - - +
712A PHE* 3.8 27.8 - - + -
1001A 4K7 4.0 18.4 - - + -
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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