Contacts of the strand formed by residues 615 - 621 (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 LEU 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A CYS* 3.7 7.9 - - - +
585A HIS 3.9 1.6 - - - -
586A MSE 3.5 26.7 - - + +
601A VAL* 4.0 27.1 - - + -
604A SER* 2.9 36.9 + - - +
605A LYS* 2.6 41.7 + - + +
613A ASN 3.6 2.0 + - - -
614A ALA* 1.3 70.3 - - - +
616A GLU* 1.3 56.3 + - - +
617A THR 3.3 27.4 - - - +
618A LEU* 4.5 9.2 - - + -
673A LEU* 3.6 21.5 - - + -
725A THR* 3.7 4.8 + - + +
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Residues in contact with GLU 616 (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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582A GLY 3.5 23.0 - - - +
583A ILE* 4.2 4.0 - - + -
584A CYS 3.0 13.6 + - - +
605A LYS* 3.7 5.0 + - - +
609A PRO 4.4 0.2 - - - +
611A ALA 4.8 1.4 - - - +
614A ALA* 3.6 17.4 - - - +
615A LEU* 1.3 79.2 - - - +
617A THR* 1.3 66.4 + - - +
666A THR 3.7 15.7 - - - +
667A GLU* 3.3 20.1 - - + +
668A TYR* 2.8 49.1 + - - +
669A GLY* 3.4 12.4 + - - -
673A LEU* 3.4 5.4 - - - +
674A CYS* 3.0 24.8 + - - +
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Residues in contact with THR 617 (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* 4.8 3.5 - - - +
584A CYS 3.2 4.6 + - - -
585A HIS* 3.3 34.5 + - + +
586A MSE 3.2 23.4 + - - -
615A LEU* 3.3 4.0 - - - +
616A GLU* 1.3 84.4 + - - +
618A LEU* 1.3 64.6 + - - +
619A LEU* 3.8 13.0 + - + -
664A LEU* 4.3 12.1 + - + -
666A THR 5.3 1.9 + - - -
668A TYR* 5.5 0.5 - - - -
674A CYS* 3.3 27.4 - - + +
676A GLU* 4.9 1.3 - - + -
687A HIS* 3.8 17.3 - - + +
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Residues in contact with LEU 618 (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 3.6 18.6 - - + +
588A VAL* 3.6 27.8 - - + -
601A VAL* 4.0 25.8 - - + -
615A LEU* 4.5 3.8 - - + -
617A THR* 1.3 71.3 - - - +
619A LEU* 1.3 61.3 + - - +
620A ILE* 3.8 21.8 + - + -
633A ILE* 4.0 24.2 - - + -
673A LEU* 3.8 14.4 - - + +
674A CYS 2.6 14.1 + - - +
675A ILE* 3.4 24.8 - - + +
676A GLU 3.1 25.6 + - - +
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Residues in contact with LEU 619 (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* 4.1 11.0 - - + -
586A MSE 2.9 13.5 + - - +
587A TYR* 3.3 13.8 - - + -
588A VAL* 2.7 33.8 + - - +
617A THR* 3.8 4.9 + - + +
618A LEU* 1.3 71.9 - - - +
620A ILE* 1.3 59.2 + - - +
676A GLU* 3.6 20.4 - - + +
678A VAL* 4.1 12.6 - - + -
684A ALA* 3.8 30.3 - - + +
687A HIS* 3.6 46.9 - - + +
688A ILE* 3.9 16.8 - - + -
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Residues in contact with ILE 620 (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 VAL* 4.0 12.6 - - + +
618A LEU* 3.8 28.0 - - + +
619A LEU* 1.3 79.2 - - - +
621A HIS* 1.4 75.6 + - - +
624A LEU* 4.1 18.8 - - + -
625A LEU* 4.7 6.1 - - + -
629A LEU* 6.2 0.9 - - + -
630A PHE* 3.7 37.2 - - + -
633A ILE* 4.6 9.0 - - + -
675A ILE* 3.7 21.3 - - + -
676A GLU 3.0 10.7 + - - +
677A VAL* 3.5 10.2 - - + +
678A VAL* 3.0 25.7 + - - -
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Residues in contact with HIS 621 (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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587A TYR* 2.8 30.1 + - - +
588A VAL 2.9 23.0 + - - +
589A ASP* 3.8 1.3 + - - -
590A SER* 3.3 38.4 + - - +
620A ILE* 1.4 83.4 - - - +
622A ARG* 1.3 70.0 + - - +
623A ASP* 2.7 51.8 + - + -
624A LEU* 3.2 14.6 + - + +
625A LEU* 3.8 1.4 - - - +
678A VAL 3.9 4.3 - - - -
679A ASP 3.4 23.9 + - - -
680A ASN* 4.0 7.9 - - + -
681A VAL* 5.2 0.7 - - + -
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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