Contacts of the strand formed by residues 644 - 650 (chain B) in PDB entry 4Y5U
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 ALA 644 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A ILE* 3.8 25.1 - - + -
590A GLN* 2.9 29.1 + - + +
592A PHE* 4.6 6.7 - - + -
605A ARG* 5.8 0.9 - - - +
648A MET* 4.2 21.3 - - + -
649A THR 3.2 10.3 - - - +
650A VAL* 4.5 1.8 - - + +
642B VAL 3.5 0.8 + - - -
643B PRO* 1.3 76.5 - - - +
645B THR* 1.3 64.4 + - - +
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Residues in contact with THR 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ARG* 5.8 0.9 - - - -
647A LYS 3.7 0.5 - - - +
648A MET* 3.3 5.5 - - - -
649A THR* 2.8 38.7 + - - -
651A GLU* 3.9 17.2 + - - -
643B PRO* 5.9 0.3 - - - +
644B ALA* 1.3 74.6 - - - +
646B ILE* 1.3 69.5 + - - +
647B LYS* 4.1 11.6 + - + -
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Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A ILE* 4.5 17.7 - - + -
600A ARG* 3.6 22.7 - - + -
605A ARG* 3.8 25.1 - - - +
646A ILE* 3.5 25.8 - - + -
647A LYS 3.5 2.5 - - - +
648A MET* 3.4 34.8 - - + -
600B ARG* 3.5 35.8 + - - +
645B THR* 1.3 77.7 - - - +
647B LYS* 1.3 61.4 + - - +
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Residues in contact with LYS 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ILE* 4.4 4.0 - - - -
647A LYS 3.1 29.1 + - - +
649A THR* 4.1 28.6 + - - +
651A GLU* 5.7 3.2 + - - -
608B ASP* 3.5 37.7 - - - +
645B THR* 4.1 12.2 + - + -
646B ILE* 1.3 76.3 - - - +
648B MET* 1.3 66.8 + - - +
649B THR* 3.2 8.9 + - - +
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Residues in contact with MET 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ALA* 4.2 11.2 - - + -
645A THR 3.5 7.4 - - - +
646A ILE* 3.7 23.3 - - + +
573B ILE* 4.9 2.0 - - + -
589B ILE* 4.5 4.3 - - + -
592B PHE* 3.7 19.7 - - + -
605B ARG* 3.7 43.5 - - + +
608B ASP* 2.9 24.3 + - + +
609B LEU* 3.3 59.0 - - + +
647B LYS* 1.3 78.8 - - - +
649B THR* 1.3 61.8 + - - +
650B VAL* 4.4 13.0 - - + -
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Residues in contact with THR 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ALA* 3.1 4.5 - - - -
645A THR* 2.6 48.4 + - - +
647A LYS* 3.5 39.0 - - - +
649A THR* 5.6 0.2 + - - -
609B LEU* 4.8 0.4 - - - -
647B LYS* 3.2 20.3 + - - +
648B MET* 1.3 75.3 + - - +
650B VAL* 1.3 74.3 + - - +
651B GLU 3.8 0.7 + - - -
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Residues in contact with VAL 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A VAL* 3.3 23.8 - - + -
643A PRO 3.7 2.9 - - - +
644A ALA* 4.3 5.6 - - + -
587B GLU* 3.6 15.5 - - - +
589B ILE* 3.8 41.3 - - + -
609B LEU* 4.6 10.7 - - + +
648B MET* 4.4 7.2 - - + -
649B THR* 1.3 87.9 - - - +
651B GLU* 1.3 68.5 + - - +
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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