Contacts of the strand formed by residues 520 - 525 (chain A) in PDB entry 2DH2
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 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LEU* 3.4 17.8 - - - +
354A LEU* 3.6 15.9 - - - +
465A VAL 3.4 6.7 - - - -
466A LEU* 4.2 0.2 - - - -
497A SER* 3.3 6.4 + - - -
498A THR* 3.0 38.8 + - - +
519A GLU* 1.3 73.2 - - - +
521A LEU* 1.3 62.8 + - - -
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Residues in contact with LEU 521 (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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354A LEU* 3.7 7.5 - - - +
463A LEU 3.8 0.3 - - - +
464A VAL* 3.4 5.5 - - - -
465A VAL* 2.8 36.3 + - + +
494A LEU* 4.1 9.9 - - + -
496A LEU 3.7 0.9 - - - -
497A SER* 3.5 28.9 - - - +
502A ARG* 3.8 19.3 - - - +
508A LEU* 4.5 5.6 - - + -
513A LEU* 3.8 33.4 - - + -
515A LEU* 3.4 28.5 - - + -
519A GLU* 3.6 13.9 - - - +
520A GLY* 1.3 72.3 - - - +
522A LEU* 1.3 59.4 + - - +
523A LEU* 3.8 14.8 - - + +
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Residues in contact with LEU 522 (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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354A LEU* 4.0 15.9 - - + +
358A THR* 4.2 12.3 - - + -
425A LEU* 4.2 14.8 - - + -
428A GLN* 4.8 11.7 - - + -
435A LEU* 5.4 1.3 - - + -
462A PHE* 3.9 28.5 - - + -
463A LEU 3.6 0.9 - - - +
464A VAL* 4.0 24.5 - - + -
494A LEU* 3.7 1.9 - - - +
495A LEU* 2.9 49.2 + - + +
496A LEU* 2.9 31.3 + - + +
521A LEU* 1.3 72.0 - - - +
523A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 523 (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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462A PHE* 3.3 8.7 - - - +
463A LEU* 2.7 51.0 + - + +
465A VAL* 4.0 17.7 - - + -
492A ALA* 3.9 27.6 - - + +
493A ASP 3.3 8.7 - - - +
494A LEU* 4.4 7.9 - - + -
495A LEU* 4.3 0.9 - - - +
508A LEU* 4.1 22.7 - - + -
510A LEU* 4.1 20.0 - - + -
513A LEU* 4.7 3.4 - - + -
521A LEU* 3.8 26.5 - - + -
522A LEU* 1.3 76.7 - - - +
524A ARG* 1.3 62.0 + - - +
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Residues in contact with ARG 524 (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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428A GLN* 4.8 4.2 + - - +
432A GLU* 4.7 12.5 + - - -
460A GLU* 3.4 25.7 - - + +
461A ARG 3.1 14.8 - - - +
462A PHE* 3.7 19.3 - - + -
492A ALA* 3.6 1.2 - - - +
493A ASP* 2.9 48.7 + - + +
494A LEU 5.4 1.4 + - - -
495A LEU* 3.8 36.1 - - + +
505A GLY* 5.7 5.1 - - - -
523A LEU* 1.3 75.4 - - - +
525A PHE* 1.3 66.4 + - - +
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Residues in contact with PHE 525 (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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453A ILE* 4.3 10.5 - - + -
460A GLU* 3.2 7.1 - - - +
461A ARG* 2.8 63.5 + - + -
463A LEU* 4.4 14.4 - - + -
486A ALA 3.6 18.8 - - - -
487A SER 3.5 20.0 - - - -
488A LEU* 4.2 14.1 - - + -
489A PRO* 3.7 36.6 - - + -
491A LYS 4.8 1.1 - - - +
492A ALA* 4.2 13.0 - - + -
524A ARG* 1.3 80.3 - - - +
526A PRO* 1.3 91.2 - - + +
528A ALA 5.4 1.3 - - - -
529A ALA 5.7 0.2 - - - -
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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