Contacts of the strand formed by residues 547 - 552 (chain B) in PDB entry 3B60
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 GLU 547 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B LEU* 4.4 7.3 - - - +
365B LYS 5.3 3.6 - - - +
371B THR 3.2 3.7 + - - +
372B VAL* 3.3 19.1 - - + +
373B ALA* 2.9 24.9 + - - +
545B ALA* 3.0 4.2 - - - +
546B ASP* 1.3 83.2 - - + +
548B ILE* 1.3 72.0 + - - +
549B VAL* 4.2 8.1 - - - +
559B ARG* 3.0 36.5 - - - +
560B GLY* 4.1 19.1 - - - +
561B THR* 5.2 0.4 - - - +
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Residues in contact with ILE 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 3.9 3.1 - - + -
375B VAL* 4.0 24.2 - - + -
542B ILE* 3.4 27.6 - - + +
545B ALA* 3.9 18.8 - - + +
547B GLU* 1.3 81.6 - - - +
549B VAL* 1.3 66.7 + - - +
550B VAL* 3.6 1.6 + - + +
558B GLU 3.1 13.0 - - - +
559B ARG* 3.3 1.7 - - - -
560B GLY 3.1 30.4 + - - +
561B THR 3.9 0.7 - - - -
562B HIS* 3.6 22.9 - - + +
565B LEU* 3.3 12.1 - - + +
572B TYR* 3.8 27.8 - - + +
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Residues in contact with VAL 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ILE* 6.5 0.2 - - + -
364B LEU* 3.8 24.9 - - + -
372B VAL* 3.6 27.6 - - + -
373B ALA 2.8 15.1 + - - +
374B LEU* 3.8 17.5 - - + -
375B VAL 3.0 23.4 + - - +
547B GLU* 4.3 8.1 - - - +
548B ILE* 1.3 72.7 - - - +
550B VAL* 1.3 61.9 + - - +
551B VAL* 3.4 5.0 + - + +
556B ILE* 3.3 38.6 - - + -
558B GLU 3.4 3.1 - - - -
559B ARG* 4.8 0.7 - - + -
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 3.3 8.7 - - + +
376B GLY* 5.2 3.4 - - - -
548B ILE* 4.6 1.8 - - + +
549B VAL* 1.3 71.4 - - - +
551B VAL* 1.3 67.0 + - - +
552B GLU* 5.9 1.1 - - + -
556B ILE* 3.7 2.8 - - - +
557B VAL* 2.8 26.8 + - + -
558B GLU* 2.7 24.3 + - + +
565B LEU* 3.2 35.7 - - + -
571B VAL* 4.1 30.1 - - + -
572B TYR* 3.6 29.4 - - + +
575B LEU* 5.5 3.4 - - + -
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Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 5.5 4.9 - - + -
362B ILE* 5.2 1.6 - - + -
374B LEU* 4.3 10.5 - - + -
375B VAL 2.8 19.5 + - - +
376B GLY* 2.9 28.9 - - - -
377B ARG 3.4 0.2 + - - -
380B SER* 2.8 27.4 + - - +
381B GLY* 4.9 2.5 - - - +
382B LYS* 3.8 24.7 - - + +
549B VAL* 4.1 10.1 - - + +
550B VAL* 1.3 79.4 - - - +
552B GLU* 1.3 63.5 + - - +
554B GLY 4.5 1.3 - - - -
555B ILE* 3.3 28.7 - - - +
556B ILE* 3.5 7.6 - - + +
557B VAL* 4.2 0.4 - - - +
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Residues in contact with GLU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ARG* 2.7 57.8 + - + +
380B SER* 3.4 3.6 - - - -
550B VAL* 5.9 2.0 - - + -
551B VAL* 1.3 75.1 - - - +
553B ASP* 1.3 82.5 + - + +
554B GLY 3.5 2.0 - - - -
555B ILE* 2.7 30.0 + - - +
557B VAL* 4.3 12.6 - - + +
571B VAL* 3.9 13.5 - - + +
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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