Contacts of the strand formed by residues 415 - 422 (chain B) in PDB entry 4CCN
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 SER 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B TYR 3.6 1.0 - - - +
329B LEU* 3.3 6.2 - - - +
330B THR* 2.8 33.6 + - - -
350B GLN* 2.8 24.8 + - - -
352B GLU 3.3 6.1 - - - -
354B ARG 3.4 14.6 - - - -
355B LYS* 3.4 24.1 - - - +
409B CYS* 3.6 12.6 - - - -
414B HIS* 1.3 83.1 - - - +
416B LEU* 1.3 61.9 + - - +
417B HIS* 4.3 2.8 - - - -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.6 3.8 - - + -
243B SER* 3.6 14.1 - - - +
244B THR* 3.6 35.0 - - - +
247B LEU* 5.3 3.4 - - + -
327B VAL* 3.7 22.2 - - + -
328B TYR 3.3 14.4 - - - +
329B LEU* 3.8 26.2 - - + -
350B GLN* 3.7 2.1 + - - -
351B LEU* 2.9 36.2 + - + -
352B GLU* 2.8 36.0 + - + +
415B SER* 1.3 76.0 + - - +
417B HIS* 1.3 63.5 + - - +
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Residues in contact with HIS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASN 3.9 0.2 - - - +
327B VAL* 3.4 5.3 - - - +
328B TYR* 2.9 56.4 + + + +
348B VAL* 3.5 11.3 - - + +
349B LEU 3.1 18.8 - - - +
350B GLN* 3.9 14.1 - - - +
351B LEU* 4.2 4.7 - - - +
355B LYS* 4.1 16.6 - - + -
357B TRP* 3.6 16.3 - + - -
415B SER* 4.5 2.2 - - - -
416B LEU* 1.3 78.0 - - - +
418B LEU* 1.3 58.3 + - - +
419B THR* 3.1 16.3 + - - -
902B OGA 2.9 51.3 + - - -
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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
----------------------------------------------------------
241B LEU* 4.8 13.7 - - + -
242B PHE* 4.9 4.3 - - + -
308B VAL* 4.1 35.9 - - + -
311B PHE* 5.8 4.9 - - + -
312B LEU* 5.7 2.5 - - + -
325B SER* 4.1 16.2 - - - +
326B ASN 3.4 9.2 - - - +
327B VAL* 4.3 15.7 - - + +
347B PHE 3.5 1.7 - - - +
349B LEU* 3.0 49.8 + - + +
351B LEU* 4.1 15.8 - - + +
417B HIS* 1.3 74.1 - - - +
419B THR* 1.3 62.1 + - - +
420B LEU* 4.0 17.3 - - + +
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Residues in contact with THR 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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325B SER* 3.0 24.1 - - - -
326B ASN 2.8 12.2 + - - -
328B TYR* 3.1 13.8 - - - -
344B ILE* 5.5 0.2 - - + -
346B ALA* 3.9 28.3 - - + -
347B PHE 3.4 7.0 - - - +
348B VAL* 4.1 6.1 - - + +
417B HIS* 3.1 14.0 + - - -
418B LEU* 1.3 72.3 - - - +
420B LEU* 1.3 61.8 + - - +
421B SER* 5.3 0.4 - - - -
902B OGA 2.8 32.6 + - - +
216D HIS* 3.4 18.5 - - + +
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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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209B LEU* 3.7 21.1 - - + -
311B PHE* 4.7 5.6 - - + -
312B LEU* 3.2 31.0 - - + -
315B LEU* 3.5 27.1 - - + -
319B PHE* 4.5 9.4 - - + -
323B ALA* 3.9 16.2 - - + -
324B GLY 3.6 8.5 - - - +
325B SER* 4.3 2.2 - - - -
345B GLU 3.3 4.2 - - - +
346B ALA* 3.5 0.9 - - - -
347B PHE* 2.8 59.2 + - + +
349B LEU* 4.6 3.8 - - + -
418B LEU* 3.8 12.8 + - + +
419B THR* 1.3 70.7 - - - +
421B SER* 1.3 61.3 + - - +
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Residues in contact with SER 421 (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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323B ALA* 3.4 2.9 - - - -
324B GLY 3.0 34.4 + - - +
344B ILE* 3.4 31.4 - - - -
345B GLU 3.2 4.7 - - - -
346B ALA* 5.2 0.4 - - - -
419B THR* 3.7 1.2 + - - -
420B LEU* 1.3 77.6 - - - +
422B THR* 1.3 65.4 + - - +
216D HIS* 3.0 24.5 + - - -
218D HIS* 2.8 25.5 + - - -
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Residues in contact with THR 422 (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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223B TRP* 3.8 27.8 - - + -
319B PHE* 3.8 35.0 - - + -
321B SER* 3.5 17.3 + - - -
322B MET 3.0 19.0 + - - -
323B ALA* 4.5 0.4 - - - -
344B ILE* 3.3 5.3 - - - +
345B GLU* 3.0 33.5 + - + +
347B PHE* 4.6 2.2 - - + -
421B SER* 1.3 79.5 - - - +
423B TYR* 1.3 72.6 + - + +
424B GLN 3.5 2.0 - - - -
218D HIS* 4.0 3.1 - - - -
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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