Contacts of the strand formed by residues 325 - 331 (chain B) in PDB entry 3CB4
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 PHE 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PRO* 4.0 17.3 - - + -
296B TYR* 3.8 20.6 - + - -
323B SER 3.4 1.2 + - - +
324B LEU* 1.3 81.6 - - - +
326B TYR* 1.3 70.0 + - - +
327B GLU* 3.5 41.5 - - + -
339B ARG* 3.9 24.5 - - - -
340B CYS* 3.2 4.5 - - - -
341B GLY* 2.7 42.6 + - - +
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Residues in contact with TYR 326 (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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311B ARG* 5.0 5.7 + - + -
314B LEU* 3.6 47.1 - - + -
315B GLY* 3.6 17.8 - - - -
318B SER* 3.3 26.2 + - - -
324B LEU* 4.4 11.9 - - + -
325B PHE* 1.3 86.1 - - - +
327B GLU* 1.3 62.3 + - - +
328B PRO* 4.7 1.8 - - + +
338B PHE* 4.0 19.7 - + + -
339B ARG 3.3 5.2 - - - -
340B CYS* 3.9 17.3 - - - -
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 3.5 30.8 - - + -
326B TYR* 1.3 76.6 - - - +
328B PRO* 1.3 82.6 - - + +
338B PHE* 3.5 5.2 - - - -
339B ARG* 2.8 67.1 + - + +
389B LYS* 4.8 8.0 + - - -
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Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 4.7 8.1 - - - +
326B TYR* 4.7 2.7 - - + +
327B GLU* 1.3 94.9 - - + +
329B GLU* 1.3 59.1 + - - +
337B GLY 4.0 1.3 - - - +
338B PHE* 3.8 22.4 - - + -
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Residues in contact with GLU 329 (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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298B GLY* 4.4 3.5 - - - -
300B PHE* 3.4 18.2 - - + -
327B GLU 3.4 0.4 + - - -
328B PRO* 1.3 75.0 - - - +
330B SER* 1.3 67.8 + - - +
331B SER* 5.0 0.2 - - - +
336B PHE* 5.6 0.2 - - - -
337B GLY 2.8 36.2 + - - +
338B PHE 4.4 1.1 - - - -
339B ARG* 3.5 48.7 - - + +
493B ASP* 4.9 6.4 - - - +
494B ALA* 3.4 36.4 + - + +
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 1.3 80.1 - - - +
331B SER* 1.3 64.3 + - - +
332B SER 4.3 0.2 + - - -
335B GLY 3.5 8.5 - - - -
336B PHE* 3.3 39.9 - - - -
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 4.0 9.7 - - - -
329B GLU* 5.0 1.2 - - - +
330B SER* 1.3 76.9 - - - +
332B SER* 1.3 65.5 + - - +
333B ALA 4.1 0.9 - - - -
334B LEU* 3.6 38.3 - - - +
335B GLY* 3.0 26.3 + - - +
491B ARG 5.9 1.1 - - - -
492B VAL* 3.7 23.7 - - - +
493B ASP 5.3 0.3 + - - -
494B ALA* 4.0 6.4 + - - +
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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