Contacts of the strand formed by residues 495 - 502 (chain B) in PDB entry 3DDN
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 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461B TYR 3.0 14.1 - - - -
463B ASP* 4.8 2.1 - - - +
489B GLU* 4.2 2.4 - - - +
490B ASP* 3.2 38.5 + - - +
493B GLY 3.2 4.9 - - - +
494B PRO* 1.3 86.5 - - - +
496B ALA* 1.3 61.7 + - - +
521B TYR* 4.3 10.3 - - - -
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Residues in contact with ALA 496 (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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460B HIS* 3.0 5.5 - - - -
461B TYR* 2.7 50.6 + - + +
463B ASP* 4.4 12.1 - - + -
487B LEU* 3.8 19.1 - - + -
488B SER 3.6 9.2 - - - +
489B GLU* 4.6 5.4 - - + -
490B ASP* 3.6 3.4 + - - -
495B GLY* 1.3 75.9 - - - +
497B THR* 1.3 64.1 + - - +
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Residues in contact with THR 497 (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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443B ILE* 5.2 7.3 + - - +
446B ARG* 3.4 26.8 - - + +
448B PHE* 3.7 21.5 - - - -
458B ILE* 5.2 4.1 - - - +
459B ILE 3.2 8.6 + - - -
460B HIS* 3.8 15.3 - - + +
487B LEU* 3.3 2.2 - - - +
488B SER 3.0 30.5 + - - +
490B ASP* 3.2 23.3 - - - +
496B ALA* 1.3 75.8 - - - +
498B ILE* 1.3 61.9 + - - +
499B LEU* 4.9 3.3 - - - +
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Residues in contact with ILE 498 (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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448B PHE* 4.9 0.2 - - - -
457B LEU 3.7 0.3 - - - +
458B ILE* 3.4 4.5 - - - +
459B ILE* 2.8 58.1 + - + +
461B TYR* 3.9 13.2 - - + -
468B LEU* 3.5 31.2 - - + -
471B ILE* 4.3 3.8 - - + -
485B ALA* 4.6 7.4 - - + -
486B GLN 3.4 17.5 - - - +
487B LEU* 3.9 16.2 - - + -
497B THR* 1.3 76.3 + - - +
499B LEU* 1.3 68.7 + - - +
500B LEU* 3.7 37.7 - - + -
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Residues in contact with LEU 499 (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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440B ILE* 4.3 25.8 - - + -
443B ILE* 4.2 19.5 - - + -
448B PHE* 4.2 19.5 - - + -
450B LEU* 3.6 32.2 - - + +
456B ASN* 5.1 11.4 - - + +
457B LEU 3.4 2.9 - - - +
458B ILE* 3.7 35.0 - - + -
485B ALA* 3.2 4.0 - - - +
486B GLN 3.0 31.3 + - - +
497B THR* 4.9 1.3 - - - +
498B ILE* 1.3 77.2 - - - +
500B LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 500 (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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455B ILE 3.7 0.2 - - - +
456B ASN* 3.1 6.6 - - - -
457B LEU* 2.7 65.7 + - + +
459B ILE* 4.2 3.6 - - + -
468B LEU* 5.6 1.3 - - + -
471B ILE* 4.4 7.2 - - + -
472B GLY* 6.1 0.4 - - - +
475B LEU* 4.2 18.6 - - + -
482B ILE* 4.2 17.0 - - + -
484B ALA 3.6 4.3 - - - +
485B ALA* 4.0 12.6 - - + -
498B ILE* 3.7 45.3 - - + -
499B LEU* 1.3 78.5 - - - +
501B ARG* 1.3 60.0 + - - +
502B LEU* 3.7 16.2 + - + +
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Residues in contact with ARG 501 (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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450B LEU* 3.9 24.1 - - + +
451B ARG* 4.0 38.4 + - - +
453B GLN* 3.4 38.0 - - - +
454B GLY* 4.5 2.9 - - - -
455B ILE 3.3 13.0 - - - +
456B ASN* 3.5 8.9 + - - +
482B ILE* 3.6 3.8 - - - -
483B GLN* 2.7 63.8 + - - +
484B ALA* 2.9 32.0 + - + +
499B LEU 4.3 0.4 + - - -
500B LEU* 1.3 72.8 - - - +
502B LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 502 (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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454B GLY* 5.4 0.7 - - - -
455B ILE* 2.9 33.7 + - + +
457B LEU* 3.4 37.7 - - + +
475B LEU* 4.7 7.4 - - + -
480B VAL* 3.6 17.5 - - + -
481B ASN 3.3 5.4 - - - +
482B ILE* 4.1 17.7 - - + -
483B GLN* 4.1 10.9 + - - +
500B LEU* 3.7 19.5 - - + -
501B ARG* 1.3 83.8 - - - +
503B ASP* 1.3 63.2 + - - +
504B GLN 3.2 14.7 + - - +
506B VAL* 3.8 21.5 - - + -
525B VAL* 5.1 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