Contacts of the strand formed by residues 416 - 420 (chain B) in PDB entry 2ID5
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 ALA 416 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B PRO 3.8 1.2 + - - -
415B PRO* 1.3 72.6 - - - +
417B ILE* 1.3 61.3 + - - +
418B LEU* 5.1 10.2 - - + +
459B ILE 3.6 1.4 - - - +
460B ALA* 3.4 3.6 - - - -
461B ALA* 3.1 37.6 + - + +
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Residues in contact with ILE 417 (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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407B CYS* 4.4 4.7 - - - +
409B ALA* 3.7 18.4 - - + +
415B PRO* 3.8 13.0 + - + +
416B ALA* 1.3 81.7 - - - +
418B LEU* 1.3 73.8 + - - +
419B TRP* 4.1 8.1 - - + +
427B VAL 4.6 0.9 - - - +
428B SER* 4.6 3.1 - - - -
429B ALA 5.0 1.9 + - - -
437B VAL* 4.1 15.0 - - + +
439B PRO 5.2 4.7 - - - +
440B ASP 4.9 2.5 - - - +
441B GLY* 3.9 37.0 - - - +
458B CYS* 3.6 26.0 - - - -
459B ILE 3.4 1.3 - - - +
460B ALA* 3.6 22.9 - - + -
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 4.1 26.0 - - + -
416B ALA* 5.1 10.1 - - + +
417B ILE* 1.3 87.0 - - - +
419B TRP* 1.3 65.9 + - - +
420B LEU 4.3 0.2 - - - -
426B LEU* 4.1 28.3 - - + -
427B VAL 3.6 3.8 - - - +
428B SER* 3.7 29.4 - - - +
457B LEU 3.5 0.7 - - - +
458B CYS* 3.5 4.9 - - - -
459B ILE* 2.7 49.8 + - + +
461B ALA* 6.2 4.0 - - + -
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Residues in contact with TRP 419 (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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393B GLN* 5.3 0.2 - - - -
405B PHE* 3.9 25.1 - - + -
406B VAL 4.1 9.4 - - - -
407B CYS* 3.5 22.2 - - + -
417B ILE* 4.1 4.3 - - + +
418B LEU* 1.3 76.0 - - - +
420B LEU* 1.3 59.7 + - - +
421B SER 3.9 0.4 - - - -
425B HIS 3.3 3.5 - - - +
426B LEU* 3.5 5.6 - - - -
427B VAL* 2.7 51.9 + - + +
437B VAL* 3.7 21.1 - - + -
441B GLY 3.1 21.3 + - - -
443B LEU* 3.4 45.4 - - + +
456B TYR* 4.0 17.0 - - + -
457B LEU 3.4 19.5 - - - -
458B CYS* 3.5 27.1 - - + -
459B ILE* 6.0 0.2 - - - -
469B MET* 5.1 1.3 - - + -
471B ALA* 4.2 14.1 - - + -
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Residues in contact with LEU 420 (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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117A VAL* 3.9 17.5 - - + -
118A ILE* 4.6 9.4 - - + -
141A VAL* 3.9 25.6 - - + -
142A TYR* 4.1 17.9 - - + -
419B TRP* 1.3 71.6 - - - +
421B SER* 1.3 71.0 + - - +
424B LYS* 4.6 3.6 - - - -
425B HIS 3.5 24.2 - - - +
426B LEU* 4.1 15.9 - - + -
455B THR 4.1 0.9 - - - +
456B TYR* 3.4 8.1 - - - -
457B LEU* 2.7 57.1 + - + +
459B ILE* 4.9 6.7 - - + +
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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