Contacts of the strand formed by residues 424 - 429 (chain B) in PDB entry 5H15
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 ILE 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 5.4 0.9 - - - -
101B PHE* 3.7 21.8 - - + -
111B LEU* 3.7 22.7 - - + -
126B CYS* 3.7 22.9 - - + -
417B SER 3.9 0.4 - - - +
418B PHE* 3.3 9.1 - - - +
419B SER* 3.0 28.4 + - - +
422B SER 4.9 0.2 - - - -
423B SER* 1.3 87.5 + - - +
425B LEU* 1.3 63.1 + - - +
426B ILE* 4.0 7.9 - - + -
436B ARG* 3.6 46.2 - - + +
437B TRP 3.4 4.0 - - - +
438B ASP* 3.6 12.8 - - - +
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Residues in contact with LEU 425 (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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82B PHE* 4.2 14.1 - - + -
378B ALA* 4.3 2.7 - - + -
386B LEU* 3.8 27.8 - - + -
388B VAL* 3.9 25.6 - - + -
404B LEU* 3.9 10.3 - - + -
416B THR* 4.0 17.7 - - - +
417B SER 3.5 15.5 - - - +
418B PHE* 3.7 38.8 - - + -
424B ILE* 1.3 73.4 - - - +
426B ILE* 1.3 62.7 + - - +
435B TRP 3.6 1.6 - - - +
436B ARG* 3.8 1.2 - - - -
437B TRP* 2.7 44.3 + - + +
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.7 27.1 - - + +
101B PHE* 3.5 26.5 - - + -
113B PHE* 3.7 25.8 - - + -
126B CYS* 4.6 0.7 - - - -
132B ILE* 5.0 2.2 - - + -
416B THR* 3.0 7.2 - - - -
417B SER 2.8 36.2 + - - +
424B ILE* 4.0 4.0 - - + -
425B LEU* 1.3 74.8 - - - +
427B ALA* 1.3 65.4 + - - +
428B VAL* 4.3 0.7 - - + -
434B ILE* 3.8 23.6 - - + -
435B TRP 3.2 6.1 - - - +
436B ARG* 3.7 35.9 - - + -
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Residues in contact with ALA 427 (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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386B LEU* 4.1 15.7 - - + -
413B ILE* 3.8 28.9 - - + -
415B GLN 3.6 5.6 - - - -
416B THR* 4.0 7.4 - - + -
425B LEU 4.2 0.2 - - - -
426B ILE* 1.3 73.9 - - - +
428B VAL* 1.4 62.8 + - - +
434B ILE* 3.5 3.8 - - - -
435B TRP* 2.9 47.5 + - + +
437B TRP* 5.2 1.3 - - + +
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Residues in contact with VAL 428 (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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96B LEU* 3.8 30.7 - - + +
98B GLY 3.9 17.7 - - - +
99B VAL* 3.7 29.2 - - + -
115B THR* 3.8 22.7 - - + -
413B ILE* 3.4 6.1 - - - +
414B ARG 3.1 23.2 + - - -
415B GLN 3.0 23.3 + - - +
426B ILE* 4.3 3.1 - - + -
427B ALA* 1.4 76.7 - - - +
429B CYS* 1.3 62.3 + - - +
433B SER 3.5 3.4 - - - -
434B ILE* 4.2 7.4 - - + -
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Residues in contact with CYS 429 (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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96B LEU* 3.1 27.8 + - - +
409B CYS* 4.2 4.0 - - - -
411B ALA* 3.9 14.8 - - + -
412B ALA 3.2 9.0 - - - +
413B ILE* 3.7 26.5 - - - -
414B ARG* 5.0 0.4 - - - -
428B VAL* 1.3 78.2 - - - +
430B ASP* 1.4 60.7 + - - +
431B ASP* 3.3 19.5 - - - +
432B ALA 3.2 11.4 + - - -
433B SER* 3.0 9.6 + - - +
435B TRP* 3.7 29.4 - - - -
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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