Contacts of the strand formed by residues 584 - 588 (chain A) in PDB entry 2H5G
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 CYS 584 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A GLY 3.3 7.3 + - - -
583A ILE* 1.3 76.4 - - - +
585A HIS* 1.3 60.9 + - - +
612A CYS 3.5 25.1 - - - -
613A ASN* 3.8 15.5 - - - +
614A ALA 3.5 15.9 - - - +
615A LEU* 3.7 3.4 - - - +
616A GLU* 3.0 27.4 + - - +
617A THR* 3.2 7.8 + - - -
695A HIS* 3.9 5.8 - - - -
696A THR* 3.1 39.5 - - - +
697A ASP* 3.9 0.2 - - - -
725A THR* 4.7 4.0 - - + -
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Residues in contact with HIS 585 (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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583A ILE* 3.8 15.9 + - + +
584A CYS* 1.3 75.0 - - - +
586A MSE 1.3 61.7 + - - +
587A TYR 4.3 0.2 - - - -
615A LEU* 3.9 2.2 - - - -
617A THR* 3.3 36.4 + - + +
619A LEU* 4.1 6.7 - - + -
664A LEU 4.9 0.4 + - - -
687A HIS* 3.5 31.2 + - - -
688A ILE* 3.6 29.3 - - + +
691A TYR* 4.4 3.2 - - - +
692A GLY* 3.4 35.5 + - - -
696A THR 4.1 0.7 - - - +
697A ASP* 2.8 31.5 + - - +
698A VAL* 2.8 26.0 + - - +
725A THR* 4.2 3.8 - - - +
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Residues in contact with MSE 586 (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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585A HIS* 1.3 75.9 - - - +
587A TYR* 1.3 62.1 + - - +
588A VAL* 4.6 1.1 - - + -
600A LEU* 4.0 15.3 - - + +
601A VAL* 3.8 37.0 - - - -
604A SER* 3.3 25.8 - - - +
615A LEU* 3.5 15.8 - - + +
617A THR 3.2 6.3 + - - -
618A LEU* 3.6 12.6 - - + +
619A LEU* 2.9 26.4 + - - +
698A VAL* 3.2 32.3 - - + +
700A VAL* 3.8 24.0 - - + -
723A ALA 4.1 7.4 - - - +
724A SER* 4.4 0.9 - - - -
725A THR* 4.5 2.7 - - + +
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Residues in contact with TYR 587 (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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585A HIS* 4.3 0.6 - - - +
586A MSE 1.3 71.9 - - - +
588A VAL* 1.3 70.5 + - - +
589A ASP* 2.7 39.1 + - + -
619A LEU* 3.3 16.4 - - + -
621A HIS* 2.8 23.7 + - - -
678A VAL* 3.7 23.8 - - + -
681A VAL* 3.6 28.8 + - + -
684A ALA* 3.6 22.0 - - + -
688A ILE* 4.9 0.7 - - + -
698A VAL 2.6 9.8 + - - +
699A ILE* 3.4 23.2 - - + -
700A VAL 2.7 32.2 + - - -
710A PHE* 3.8 23.1 - + + -
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Residues in contact with VAL 588 (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 MSE 4.6 6.7 - - + -
587A TYR* 1.3 73.1 - - - +
589A ASP* 1.3 62.9 + - - +
592A ALA* 3.8 20.6 - - + -
597A VAL* 4.1 28.7 - - + -
601A VAL* 4.8 0.7 - - + -
618A LEU* 3.6 28.7 - - + -
619A LEU 2.7 12.6 + - - +
620A ILE* 4.5 12.1 - - + -
621A HIS* 2.9 29.1 + - - +
624A LEU* 3.9 12.2 - - + +
629A LEU* 4.2 7.6 - - + -
633A ILE* 4.6 3.8 - - + -
700A VAL* 3.9 7.0 - - + -
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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