Contacts of the helix formed by residues 546 - 557 (chain A) in PDB entry 2W93
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 PRO 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A GLN* 3.3 22.0 - - + +
368A GLU* 3.5 7.9 - - - +
371A TRP* 4.4 3.6 - - + -
390A THR* 4.3 7.9 - - - +
393A PHE* 3.9 6.5 - - + -
394A GLY* 3.8 23.3 - - - +
397A GLN* 3.5 21.3 - - - +
545A ALA* 1.3 95.0 - - + +
547A GLN* 1.3 64.4 + - - +
548A ASN* 3.3 22.9 - - - +
549A LEU* 3.3 5.7 + - + -
550A VAL* 3.1 20.0 + - - +
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Residues in contact with GLN 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A GLU* 2.8 28.2 + - - +
397A GLN* 3.8 2.2 + - - +
546A PRO* 1.3 71.9 - - - +
548A ASN* 1.3 59.0 + - - +
550A VAL* 3.3 19.9 + - - +
551A GLU* 2.9 54.9 + - - +
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Residues in contact with ASN 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A VAL* 5.5 3.0 - - - +
267A LEU* 3.5 49.3 + - + +
393A PHE* 2.9 40.4 + - - +
396A ASN* 4.0 14.6 - - - +
397A GLN* 3.3 20.0 + - - +
546A PRO* 3.3 18.5 - - - +
547A GLN* 1.3 77.8 - - - +
549A LEU* 1.3 76.3 + - - +
551A GLU* 3.6 6.6 - - - +
552A GLN 3.4 15.2 + - - -
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A THR* 3.8 32.5 - - + -
393A PHE* 3.8 42.0 - - + -
476A ILE* 3.9 25.8 - - + +
479A LEU* 4.1 15.0 - - + -
480A ILE* 5.8 5.8 - - + -
545A ALA* 4.1 5.8 - - + -
546A PRO* 3.3 11.6 + - + +
547A GLN 3.2 0.2 - - - -
548A ASN* 1.3 85.6 + - - +
550A VAL* 1.3 65.5 + - - +
551A GLU 3.1 1.3 - - - -
552A GLN* 3.3 9.8 + - + +
553A ALA* 3.0 23.4 + - + +
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Residues in contact with VAL 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A LEU* 5.2 8.3 - - + -
543A PHE 5.6 3.8 - - - +
545A ALA* 4.4 17.9 - - + +
546A PRO 3.1 17.4 + - - +
547A GLN* 3.3 21.5 + - - +
549A LEU* 1.3 75.8 - - - +
551A GLU* 1.3 65.3 + - - +
553A ALA* 3.3 9.0 - - - +
554A LYS* 3.2 35.6 + - + +
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Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A THR* 4.8 12.1 - - - +
267A LEU* 4.7 7.0 - - + -
547A GLN* 2.9 48.1 + - + +
548A ASN* 3.6 9.0 - - - +
549A LEU 3.1 0.2 - - - -
550A VAL* 1.3 79.6 - - - +
552A GLN* 1.3 57.6 + - - +
554A LYS* 3.1 29.2 + - - +
555A LEU* 3.1 20.8 + - + +
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 3.7 28.8 - - + +
393A PHE* 3.6 25.7 - - - -
548A ASN 3.4 7.4 + - - +
549A LEU* 3.3 10.7 + - + +
551A GLU* 1.3 76.2 - - - +
553A ALA* 1.3 56.0 + - - +
555A LEU* 3.7 15.9 - - + -
556A THR* 2.8 43.2 + - - +
114B HIS* 6.1 2.8 - - - -
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Residues in contact with ALA 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A LEU* 4.1 31.4 - - + +
480A ILE* 5.5 7.7 - - + +
549A LEU* 3.0 15.5 + - + +
550A VAL* 3.3 14.6 - - - +
551A GLU 3.2 0.2 - - - -
552A GLN* 1.3 78.7 - - - +
554A LYS* 1.3 75.9 + - - +
556A THR* 3.6 6.2 + - - -
557A ALA* 2.9 22.0 + - - +
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Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A LEU 5.2 3.6 + - - -
550A VAL* 3.2 30.3 - - + +
551A GLU* 3.1 17.4 + - - +
553A ALA* 1.3 110.9 + - - +
555A LEU* 1.3 62.0 + - - +
557A ALA* 3.2 30.5 - - + +
558A ALA* 3.3 13.2 + - - +
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A THR* 3.4 35.9 - - + +
267A LEU* 4.0 6.7 - - + -
551A GLU* 3.1 15.0 + - + +
552A GLN* 3.6 30.1 - - + +
554A LYS* 1.3 74.7 - - - +
556A THR* 1.3 63.5 + - - +
557A ALA 3.2 8.1 - - - +
558A ALA* 5.0 2.3 - - - +
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Residues in contact with THR 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A ILE* 4.0 30.5 - - + +
552A GLN* 2.8 29.4 + - - +
553A ALA* 3.9 7.1 - - - -
555A LEU* 1.3 71.4 - - - +
557A ALA* 1.3 66.8 + - - +
559A THR* 5.0 5.2 - - - +
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Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A ALA 2.9 18.3 + - - +
554A LYS* 3.2 23.3 - - + +
555A LEU 3.2 8.9 - - - +
556A THR* 1.3 82.5 - - - +
558A ALA* 1.3 71.9 + - - +
559A THR* 3.1 10.8 + - - -
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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