Contacts of the helix formed by residues 546 - 562 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D GLN* 3.5 21.0 - - + +
368D GLU* 5.6 8.3 - - + +
371D TRP* 4.0 5.8 - - + +
390D THR* 3.7 13.2 - - + +
393D PHE* 4.0 3.6 - - + -
394D GLY* 3.5 31.0 - - - +
397D GLN* 3.6 13.0 - - - +
545D ALA* 1.3 90.0 - - + +
547D GLN* 1.3 64.7 + - - +
548D ASN* 3.1 18.2 - - - +
549D LEU* 3.1 16.7 + - + +
550D VAL* 3.3 9.5 + - - +
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Residues in contact with GLN 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D GLU* 4.9 13.8 + - - +
545D ALA 4.0 10.0 - - - +
546D PRO* 1.3 69.8 - - - +
548D ASN* 1.3 65.2 + - - +
550D VAL* 3.2 30.4 + - - +
551D GLU* 3.2 22.3 + - - +
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Residues in contact with ASN 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 6.1 3.7 - - + +
267D LEU* 3.7 33.9 - - + +
393D PHE* 3.1 38.1 + - + -
396D ASN* 3.7 12.7 - - - +
397D GLN* 3.5 17.9 - - - +
546D PRO* 3.1 26.5 - - - +
547D GLN* 1.3 74.6 + - - +
549D LEU* 1.3 56.4 + - - -
551D GLU* 3.6 3.2 + - - -
552D GLN* 2.9 28.6 + - - +
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Residues in contact with LEU 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D PHE* 6.5 0.2 - - + -
390D THR* 3.8 41.7 - - + +
393D PHE* 3.6 46.7 - - + -
476D ILE* 3.7 31.9 - - + -
479D LEU* 4.4 9.0 - - + -
480D ILE* 6.0 0.4 - - + -
545D ALA* 4.5 4.9 - - + -
546D PRO* 3.1 13.8 + - + +
548D ASN* 1.3 77.6 + - - +
550D VAL* 1.3 59.8 + - - +
552D GLN* 4.2 0.9 - - + -
553D ALA* 2.8 47.4 + - + +
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Residues in contact with VAL 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D LEU* 4.0 30.3 - - + +
543D PHE 5.8 1.1 - - - +
545D ALA* 4.1 10.3 - - + +
546D PRO 3.5 13.9 - - - +
547D GLN* 3.2 32.3 + - - +
549D LEU* 1.3 80.0 - - - +
551D GLU* 1.3 59.4 + - - +
553D ALA* 3.6 4.6 - - - +
554D LYS* 3.4 42.1 + - - +
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Residues in contact with GLU 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D THR* 5.6 0.3 + - - -
267D LEU* 3.8 23.0 - - + +
547D GLN 3.2 14.5 + - - +
548D ASN* 4.0 0.9 - - - +
549D LEU 3.1 0.4 - - - -
550D VAL* 1.3 77.1 - - + +
552D GLN* 1.3 66.1 + - - +
554D LYS* 3.2 20.2 + - + +
555D LEU* 3.1 45.5 + - - +
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Residues in contact with GLN 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 3.8 7.7 - - + +
291D ASP* 3.7 5.1 + - - +
292D PHE* 3.6 35.9 - - + +
295D GLY* 3.3 28.4 + - - -
296D SER* 2.9 27.8 + - - +
393D PHE* 3.8 19.9 - - + -
548D ASN 2.9 20.4 + - - +
549D LEU* 3.8 4.3 - - + +
551D GLU* 1.3 75.3 - - - +
553D ALA* 1.3 58.2 + - - +
555D LEU* 2.9 10.0 + - - +
556D THR* 2.8 46.6 + - - -
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Residues in contact with ALA 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D ILE 4.6 0.2 - - - +
479D LEU* 3.6 33.2 - - + +
480D ILE* 3.7 26.7 - - + +
549D LEU* 2.8 28.4 + - + +
550D VAL 3.6 6.1 - - - +
552D GLN* 1.3 71.9 - - - +
554D LYS* 1.3 58.6 + - - +
556D THR* 3.5 3.4 + - - -
557D ALA* 3.0 29.5 + - - +
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Residues in contact with LYS 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D LEU 5.0 9.2 - - - +
480D ILE 6.0 0.2 - - - -
550D VAL* 3.4 32.5 + - - +
551D GLU* 3.2 22.1 + - + +
552D GLN 3.2 0.6 - - - -
553D ALA* 1.3 77.8 - - - +
555D LEU* 1.3 64.9 + - + +
557D ALA* 3.6 5.5 + - - +
558D ALA* 3.2 23.7 + - - +
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Residues in contact with LEU 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D THR* 5.7 1.3 - - - +
267D LEU* 4.6 6.3 - - + -
295D GLY* 3.7 30.3 - - - +
296D SER* 3.6 17.9 - - - +
551D GLU* 3.1 42.4 + - - +
552D GLN* 2.9 17.3 + - - +
554D LYS* 1.3 75.8 - - - +
556D THR* 1.3 57.5 + - - +
558D ALA* 3.5 6.0 + - - +
559D THR* 3.0 32.0 + - - -
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Residues in contact with THR 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 3.2 34.1 - - + +
114C HIS* 4.1 11.4 - - + -
291D ASP* 4.6 3.2 + - - +
292D PHE* 3.3 16.4 - - + -
296D SER* 4.6 1.9 + - - -
480D ILE* 4.6 9.2 - - + -
552D GLN* 2.8 31.2 + - - -
553D ALA* 3.9 6.5 - - - -
555D LEU* 1.3 74.9 - - - +
557D ALA* 1.3 66.4 + - - +
559D THR* 3.3 7.8 + - - -
560D ASN* 3.1 26.3 + - - +
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Residues in contact with ALA 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480D ILE* 3.6 32.0 - - + +
481D HIS* 5.5 1.6 - - + +
553D ALA 3.0 18.3 + - - +
554D LYS* 4.0 5.8 - - - +
556D THR* 1.3 76.0 - - - +
558D ALA* 1.3 61.9 + - - +
560D ASN* 3.3 7.6 + - - +
561D ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D LYS 3.2 15.5 + - - +
555D LEU* 3.7 6.7 - - + +
556D THR 3.2 0.2 - - - -
557D ALA* 1.3 75.8 - - - +
559D THR* 1.3 64.8 + - - +
561D ALA* 3.3 4.8 + - - +
562D LYS* 3.0 36.6 + - - +
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Residues in contact with THR 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C SER* 3.5 13.7 + - - -
105C SER* 5.0 0.5 + - - -
106C SER* 3.4 20.1 + - - +
111C LEU* 4.2 16.5 - - + +
113C LEU* 4.6 13.5 - - + -
296D SER* 4.8 7.8 + - - -
297D PHE* 6.4 0.4 - - + -
555D LEU 3.0 16.2 + - - -
556D THR* 3.5 11.3 - - - -
558D ALA* 1.3 76.3 - - - +
560D ASN* 1.3 69.3 + - - +
561D ALA 3.6 0.2 + - - -
562D LYS* 3.6 27.3 + - - +
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Residues in contact with ASN 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 2.8 48.0 + - - +
29C PHE* 3.2 28.2 - - - -
102C PRO* 5.1 1.2 - - - +
103C SER* 3.6 11.4 + - - -
106C SER* 5.1 1.6 + - - -
113C LEU* 5.4 0.3 - - - +
114C HIS* 5.4 0.3 - - - -
169C ALA* 3.5 17.1 - - + +
170C ASN 3.4 22.0 + - - -
480D ILE* 5.4 0.6 - - - +
556D THR* 3.1 19.9 + - - +
557D ALA* 3.7 6.7 - - - +
558D ALA 3.2 0.4 - - - -
559D THR* 1.3 83.6 - - - +
561D ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ALA 5.3 1.8 - - - -
170C ASN* 4.1 6.0 - - - +
173C ASP* 5.9 3.4 - - - +
557D ALA 3.1 16.1 + - - +
558D ALA* 4.1 4.5 - - - +
560D ASN* 1.3 76.0 - - + +
562D LYS* 1.3 62.9 + - - +
563D GLN* 3.3 19.4 + - - +
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Residues in contact with LYS 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C SER* 4.0 4.0 - - - -
105C SER* 3.6 17.8 + - - +
109C LYS* 5.2 12.6 - - - +
170C ASN* 3.5 15.7 - - - +
558D ALA* 3.0 20.7 + - - +
559D THR* 3.7 32.6 + - - +
560D ASN 3.4 1.2 - - - -
561D ALA* 1.3 74.9 - - - +
563D GLN* 1.3 74.1 + - - +
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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