Contacts of the helix formed by residues 438 - 452 (chain B) in PDB entry 1IW1
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 SER 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B LEU* 2.9 16.7 + - - +
435B GLY 3.0 1.8 + - - -
436B ASP 3.1 0.2 - - - -
437B LEU* 1.3 76.6 - - - +
439B GLY* 1.3 67.7 + - - -
440B GLY 3.2 0.2 - - - -
441B GLN* 3.0 22.0 + - - +
442B VAL* 3.8 5.6 + - - +
473B LYS* 3.3 28.6 + - - +
477B ARG* 5.1 2.3 + - - -
902B HEM 3.5 38.9 - - - +
913B SO4 5.3 0.5 + - - -
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLY 3.0 5.5 + - - -
438B SER* 1.3 80.8 - - - +
440B GLY* 1.3 62.3 + - - +
442B VAL* 3.0 10.4 + - - +
443B ILE* 2.9 29.2 + - - +
902B HEM 3.3 42.2 + - - +
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Residues in contact with GLY 440 (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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435B GLY 2.9 12.2 + - - -
436B ASP* 3.5 14.8 + - - -
438B SER 3.2 0.2 - - - -
439B GLY* 1.3 76.7 - - - +
441B GLN* 1.3 56.7 + - - +
443B ILE* 3.3 8.8 + - - +
444B ALA* 2.9 24.4 + - - +
461B TYR* 3.0 33.1 - - - -
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 5.2 6.6 - - - +
436B ASP 2.9 22.2 + - - -
437B LEU* 3.6 18.9 - - - +
438B SER 3.0 14.3 + - - +
440B GLY* 1.3 77.4 - - - +
442B VAL* 1.3 63.0 + - + +
444B ALA* 3.6 5.2 + - - +
445B ARG* 3.3 40.5 + - - +
461B TYR* 2.8 30.7 + - - +
462B HIS* 5.4 0.2 - - - -
463B PHE* 4.3 6.7 - - - -
469B LEU* 3.9 23.4 - - + +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A SO4 5.5 2.5 - - - +
438B SER 4.2 8.7 - - - +
439B GLY* 3.0 14.1 + - - +
441B GLN* 1.3 76.3 - - + +
443B ILE* 1.3 66.5 + - - +
445B ARG* 3.1 27.3 + - - +
446B MET* 3.0 33.1 + - + +
902B HEM 3.8 34.5 - - + -
911B SO4 4.0 17.3 - - - +
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Residues in contact with ILE 443 (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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329B MET* 4.0 23.6 - - + -
332B LEU* 6.0 0.7 - - + -
333B LEU* 4.1 28.0 - - + -
342B PHE* 5.0 1.8 - - + -
345B LEU* 6.0 0.4 - - + -
439B GLY 2.9 19.4 + - - +
440B GLY* 3.5 15.0 - - - +
442B VAL* 1.3 76.3 - - - +
444B ALA* 1.3 63.6 + - - +
446B MET* 3.1 4.3 + - - +
447B MET* 3.0 31.4 + - + +
461B TYR* 3.5 26.7 - - + +
902B HEM 4.1 29.6 - - + -
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 6.1 1.1 - - - +
440B GLY 2.9 16.3 + - - +
441B GLN* 3.8 6.3 - - - +
443B ILE* 1.3 75.5 - - - +
445B ARG* 1.3 63.2 + - + +
447B MET 3.3 1.7 + - - -
448B GLN* 3.2 18.5 + - - +
458B LEU* 3.7 26.2 - - + +
461B TYR* 3.6 33.9 - - + -
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Residues in contact with ARG 445 (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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111A ASN* 4.7 18.2 + - - +
114A GLU* 6.3 3.6 - - - -
115A GLU* 6.4 3.8 - - + +
118A ASP* 4.7 5.8 - - - +
914A SO4 3.8 15.1 + - - -
441B GLN* 3.3 33.7 + - - +
442B VAL* 3.1 29.2 + - - +
444B ALA* 1.3 76.7 - - + +
446B MET* 1.3 67.5 + - + +
448B GLN* 3.3 6.5 + - - +
449B ARG* 2.8 51.8 + - - +
911B SO4 2.8 48.3 + - - -
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Residues in contact with MET 446 (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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333B LEU* 3.9 27.4 - - + +
442B VAL* 3.0 26.2 + - + +
443B ILE* 3.1 8.9 + - - +
445B ARG* 1.3 81.8 - - + +
447B MET* 1.3 66.1 + - + +
449B ARG* 3.4 43.3 - - - +
450B HIS* 2.8 55.4 + - - +
911B SO4 4.7 7.9 - - - +
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Residues in contact with MET 447 (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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332B LEU* 3.6 34.3 - - + +
333B LEU* 3.7 25.1 - - + -
342B PHE* 3.6 40.4 - - + -
443B ILE* 3.0 16.2 + - + +
444B ALA 3.3 6.3 + - - +
446B MET* 1.3 80.2 - - + +
448B GLN* 1.3 65.4 + - - +
451B TYR* 3.0 43.6 + - + +
452B GLY 3.4 4.2 + - - -
453B VAL* 3.6 13.7 + - + +
458B LEU* 4.2 15.0 - - + -
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Residues in contact with GLN 448 (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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118A ASP* 3.0 31.8 + - + +
119A ASN* 3.0 31.8 + - - +
444B ALA 3.2 9.9 + - - +
445B ARG* 3.6 8.7 - - - +
447B MET* 1.3 79.2 - - - +
449B ARG* 1.3 62.5 + - + +
452B GLY* 3.0 26.5 + - - -
453B VAL 3.5 24.0 - - - +
455B PRO* 3.5 19.2 - - - +
458B LEU* 4.1 9.7 - - + +
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Residues in contact with ARG 449 (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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114A GLU* 5.7 2.4 + - - +
117A ARG* 4.0 13.7 - - - +
118A ASP* 3.0 33.2 + - + -
445B ARG* 2.8 30.7 + - - +
446B MET* 3.4 33.1 - - + +
448B GLN* 1.3 83.1 - - + +
450B HIS* 1.3 64.6 + - + +
452B GLY 4.9 0.5 + - - -
911B SO4 2.8 32.5 + - - -
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Residues in contact with HIS 450 (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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332B LEU 4.7 0.4 - - - -
333B LEU 2.8 29.9 + - - -
334B LYS* 3.5 17.6 + - - -
335B GLY* 3.5 25.5 - - - +
446B MET* 2.8 45.8 + - - +
449B ARG* 1.3 80.4 + - + +
451B TYR* 1.3 72.4 + - + +
452B GLY 3.8 0.4 - - - -
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Residues in contact with TYR 451 (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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332B LEU* 2.7 40.5 + - + -
335B GLY* 3.2 23.1 - - - -
337B LEU* 3.1 40.1 + - - +
338B GLY* 3.7 19.9 + - - -
339B VAL* 3.8 28.4 - - + +
342B PHE* 5.4 0.7 - - + -
447B MET* 3.0 42.1 + - + +
450B HIS* 1.3 85.2 - - + +
452B GLY* 1.3 64.1 + - - +
453B VAL* 3.3 5.1 + - + -
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Residues in contact with GLY 452 (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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447B MET 3.4 0.2 + - - -
448B GLN* 3.0 18.3 + - - -
449B ARG 4.7 0.2 - - - -
450B HIS 3.8 1.0 - - - -
451B TYR* 1.3 77.5 - - - +
453B VAL* 1.3 66.9 + - - +
454B ASP* 3.4 12.3 + - - +
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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