Contacts of the strand formed by residues 599 - 606 (chain A) in PDB entry 2Y48
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 GLY 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A TYR 3.6 0.2 - - - -
596A THR* 2.7 41.8 + - - +
597A ALA 3.6 0.2 - - - -
598A SER* 1.3 83.7 + - - +
600A CYS* 1.3 61.5 + - - -
618A CYS 3.6 9.2 - - - -
619A ASP* 4.9 0.4 - - - -
795A ARG* 3.7 14.7 - - - +
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Residues in contact with CYS 600 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A ARG 2.9 12.8 - - - +
595A TYR* 3.8 16.6 - - - -
599A GLY* 1.3 78.1 - - - -
601A GLU* 1.3 62.8 + - - +
616A TYR 3.6 0.2 - - - +
617A LYS* 3.4 6.9 - - - +
618A CYS* 2.8 41.4 + - - +
619A ASP 4.0 9.2 - - - -
620A ALA* 4.0 4.0 - - - -
621A VAL* 3.6 31.6 - - + -
795A ARG* 3.9 18.4 - - - -
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Residues in contact with GLU 601 (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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592A GLN 4.1 0.3 - - - +
593A VAL* 3.9 0.9 - - - +
594A ARG* 2.7 68.0 + - + +
600A CYS* 1.3 74.4 - - - +
602A VAL* 1.3 63.8 + - - +
603A ILE* 4.2 3.4 + - + +
615A ILE* 3.9 19.5 - - + +
616A TYR 2.8 9.9 - - - +
617A LYS* 3.1 37.8 + - - +
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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
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282A ILE* 3.6 26.2 - - + -
284A ILE* 4.6 1.1 - - + -
307A LEU* 3.6 26.0 - - + -
590A VAL* 3.7 26.7 - - + -
592A GLN 3.5 4.0 - - - +
593A VAL* 4.3 7.2 - - + -
601A GLU* 1.3 76.4 - - - +
603A ILE* 1.3 65.2 + - - +
615A ILE* 3.5 3.0 - - - -
616A TYR* 2.7 50.0 + - + +
618A CYS* 4.6 1.8 - - - -
621A VAL* 4.0 25.1 - - + -
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Residues in contact with ILE 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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590A VAL 3.7 0.2 - - - -
591A ARG* 2.7 36.0 + - + +
592A GLN* 2.9 53.3 + - + +
594A ARG* 4.5 10.1 - - - +
601A GLU* 5.0 6.5 - - - +
602A VAL* 1.3 75.1 - - - +
604A ALA* 1.3 55.1 + - - +
605A VAL* 5.8 1.6 - - + -
613A THR* 3.9 15.9 - - + -
614A PHE 3.3 15.0 - - - +
615A ILE* 3.8 23.1 - - + -
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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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307A LEU* 4.3 14.4 - - + -
588A THR* 3.6 27.8 - - + -
589A ALA 3.4 16.4 - - - +
590A VAL* 3.9 5.8 - - - +
602A VAL 3.9 1.8 + - - -
603A ILE* 1.3 73.9 - - - +
605A VAL* 1.3 70.3 + - - +
613A THR* 3.9 2.8 - - - +
614A PHE* 3.0 30.0 + - + +
616A TYR* 4.5 7.4 - - + -
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Residues in contact with VAL 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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588A THR* 3.2 7.8 - - - +
589A ALA* 2.8 38.1 + - + +
591A ARG* 3.5 52.5 - - + +
603A ILE* 5.8 1.3 - - + -
604A ALA* 1.3 80.4 - - - +
606A ASN* 1.3 71.9 + - - +
607A THR* 4.7 1.6 - - + +
610A THR* 4.2 16.6 - - - +
612A GLN 3.9 9.9 - - - +
613A THR* 4.3 15.5 - - + +
614A PHE* 4.3 5.8 - - - -
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Residues in contact with ASN 606 (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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586A LEU 5.3 0.2 - - - +
587A ASN 3.5 9.4 - - - +
605A VAL* 1.3 74.2 - - - +
607A THR* 1.3 67.6 + - - +
608A ARG* 3.1 42.7 + - - +
609A SER* 3.0 52.6 + - - +
610A THR* 3.2 12.0 - - - -
612A GLN* 3.4 26.5 + - + +
614A PHE* 4.2 12.0 - - + -
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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