Contacts of the helix formed by residues 546 - 562 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B GLN* 3.5 19.9 - - + +
368B GLU* 5.6 7.2 - - + +
371B TRP* 4.2 4.7 - - + +
390B THR* 3.8 13.2 - - + +
393B PHE* 3.9 5.4 - - + -
394B GLY* 3.5 31.0 - - - +
397B GLN* 3.8 11.0 - - - +
545B ALA* 1.3 91.1 - - + +
547B GLN* 1.3 65.2 + - + +
548B ASN* 3.1 20.6 - - - +
549B LEU* 3.0 17.6 + - + +
550B VAL* 3.3 8.8 + - - +
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Residues in contact with GLN 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 3.3 36.0 + - + +
545B ALA 3.5 6.5 + - - +
546B PRO* 1.3 71.8 - - - +
548B ASN* 1.3 63.4 + - - +
550B VAL* 3.2 22.2 + - - +
551B GLU* 3.3 18.1 + - - +
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Residues in contact with ASN 548 (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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264B VAL* 5.9 5.0 - - + +
267B LEU* 3.5 42.6 - - + +
393B PHE* 3.2 37.7 + - - -
396B ASN* 3.9 11.1 - - - +
397B GLN* 3.2 20.0 - - - +
546B PRO* 3.1 22.2 - - - +
547B GLN* 1.3 74.6 + - - +
549B LEU* 1.3 55.7 + - - +
551B GLU* 3.5 1.4 + - - +
552B GLN* 2.9 28.8 + - - +
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Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 5.8 0.7 - - + -
390B THR* 3.8 41.3 - - + +
393B PHE* 3.5 50.0 - - + -
476B ILE* 3.7 31.0 - - + -
479B LEU* 4.3 7.6 - - + -
545B ALA* 4.3 7.0 - - + -
546B PRO* 3.0 13.6 + - + +
548B ASN* 1.3 77.6 - - - +
550B VAL* 1.3 62.0 + - - +
552B GLN* 4.1 4.3 - - + -
553B ALA* 2.8 36.2 + - + +
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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
----------------------------------------------------------
479B LEU* 4.1 31.3 - - + +
543B PHE 5.7 1.6 - - - +
545B ALA* 4.3 10.5 - - + +
546B PRO 3.7 13.0 - - - +
547B GLN* 3.2 16.7 + - - +
549B LEU* 1.3 79.1 - - - +
551B GLU* 1.3 71.4 + - - +
553B ALA* 3.7 4.4 + - - +
554B LYS* 3.5 29.0 + - - +
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Residues in contact with GLU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.8 24.9 - - + -
547B GLN 3.3 11.1 + - - +
548B ASN* 4.0 2.5 - - - +
549B LEU 3.2 0.2 - - - -
550B VAL* 1.3 84.5 - - - +
552B GLN* 1.3 65.7 + - - +
554B LYS* 3.2 33.2 + - - +
555B LEU* 3.0 31.0 + - + +
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Residues in contact with GLN 552 (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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267B LEU* 3.9 6.5 - - + +
291B ASP* 3.7 5.7 + - - +
292B PHE* 3.6 36.4 - - + +
295B GLY* 3.4 28.2 - - - -
296B SER* 3.0 26.8 + - - +
393B PHE* 3.7 19.6 - - + -
548B ASN 2.9 19.0 + - - +
549B LEU* 3.2 5.6 + - + +
551B GLU* 1.3 76.3 - - - +
553B ALA* 1.3 57.1 + - - +
555B LEU* 3.2 9.1 + - - +
556B THR* 2.8 39.7 + - - -
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Residues in contact with ALA 553 (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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476B ILE 4.5 1.3 - - - +
479B LEU* 3.5 37.7 - - + +
480B ILE* 3.7 21.8 - - + -
549B LEU* 2.8 25.5 + - + +
550B VAL 3.7 5.6 - - - +
552B GLN* 1.3 73.7 - - - +
554B LYS* 1.3 57.1 + - - +
556B THR* 3.3 4.7 + - - -
557B ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LEU 4.7 2.8 + - - +
480B ILE 5.8 0.4 - - - -
550B VAL* 3.5 19.7 + - - +
551B GLU* 3.2 38.4 + - - +
553B ALA* 1.3 75.3 - - - +
555B LEU* 1.3 67.4 + - + +
557B ALA* 3.4 5.8 + - - +
558B ALA* 3.0 24.8 + - + +
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Residues in contact with LEU 555 (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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266B THR* 5.5 2.7 - - - +
267B LEU* 4.9 10.5 - - + -
295B GLY* 3.7 27.1 - - - +
296B SER* 3.7 20.6 - - - +
551B GLU* 3.0 22.8 + - + +
552B GLN* 3.4 14.1 - - - +
554B LYS* 1.3 76.5 - - + +
556B THR* 1.3 58.4 + - - +
558B ALA* 3.4 6.4 + - + +
559B THR* 3.0 32.8 + - - -
562B LYS* 5.2 0.2 + - - -
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Residues in contact with THR 556 (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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28A ASP* 3.2 35.0 - - + +
114A HIS* 4.3 9.4 - - + -
291B ASP* 4.6 3.6 + - - -
292B PHE* 3.4 14.7 - - + -
296B SER* 4.5 1.6 + - - -
480B ILE* 4.3 11.2 - - + -
552B GLN* 2.8 32.8 + - - +
553B ALA* 3.7 6.3 - - - -
555B LEU* 1.3 74.3 - - - +
557B ALA* 1.3 65.9 + - - +
559B THR* 3.3 7.7 + - - -
560B ASN* 3.2 27.5 + - - +
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Residues in contact with ALA 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ILE* 3.5 33.8 - - + +
481B HIS* 5.5 3.1 - - + +
553B ALA 2.9 17.8 + - - +
554B LYS* 3.8 6.5 - - - +
556B THR* 1.3 72.9 - - - +
558B ALA* 1.3 63.5 - - - +
560B ASN* 3.2 8.1 + - - +
561B ALA* 3.1 25.3 + - - +
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Residues in contact with ALA 558 (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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554B LYS 3.0 17.0 + - - +
555B LEU* 3.6 7.0 - - + +
557B ALA* 1.3 74.3 - - - +
559B THR* 1.3 64.7 + - - +
561B ALA* 3.4 4.6 + - - +
562B LYS* 3.1 39.6 + - + +
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Residues in contact with THR 559 (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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103A SER* 3.4 14.4 + - - -
105A SER* 4.7 0.3 + - - -
106A SER* 3.4 19.6 + - - +
111A LEU* 4.0 18.8 - - + -
113A LEU* 4.6 11.4 - - + -
296B SER* 4.8 8.7 + - - -
297B PHE* 6.1 1.4 - - + -
555B LEU 3.0 18.6 + - - -
556B THR* 3.6 8.2 - - - -
558B ALA* 1.3 76.1 - - - +
560B ASN* 1.3 67.1 + - - +
562B LYS* 3.5 30.5 + - - +
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Residues in contact with ASN 560 (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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28A ASP* 2.8 48.1 + - - +
29A PHE* 3.4 26.3 - - - -
103A SER* 3.6 14.9 + - - -
106A SER* 5.0 2.1 + - - -
113A LEU* 5.3 0.5 - - - +
114A HIS* 5.6 0.3 - - - -
169A ALA* 3.6 14.0 - - + +
170A ASN 3.5 21.7 + - - -
480B ILE* 5.4 0.6 - - - +
556B THR* 3.2 17.7 + - - +
557B ALA* 3.7 8.9 - - - +
558B ALA 3.2 0.2 - - - -
559B THR* 1.3 87.4 - - - +
561B ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 561 (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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169A ALA 5.5 1.3 - - - -
170A ASN* 4.4 4.3 - - - +
173A ASP* 5.5 7.6 - - - +
557B ALA 3.1 16.2 + - - +
558B ALA* 4.3 4.0 - - - +
560B ASN* 1.3 76.5 - - - +
562B LYS* 1.3 66.0 + - - +
563B GLN* 3.3 21.8 + - - +
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Residues in contact with LYS 562 (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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103A SER* 4.1 2.3 - - - -
105A SER* 3.7 20.8 + - - +
109A LYS* 5.7 7.2 - - - +
170A ASN* 3.4 16.5 + - - +
555B LEU 5.2 0.2 + - - -
558B ALA* 3.1 26.8 + - + +
559B THR* 3.5 36.9 + - - +
560B ASN 3.3 0.6 - - - -
561B ALA* 1.3 74.4 - - - +
563B GLN* 1.3 67.4 + - - +
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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
------------------------------------------------------------
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