Contacts of the helix formed by residues 436 - 451 (chain B) in PDB entry 5IYB
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 LYS 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE 4.5 0.5 - - - +
411B LEU* 3.8 9.5 - - + +
414B GLU* 3.6 34.4 - - + +
418B TYR* 3.7 27.3 - - - +
433B LEU 3.7 7.8 + - - -
434B ALA 2.9 21.5 + - - +
435B ILE* 1.3 78.8 - - - +
437B THR* 1.3 64.8 + - - +
438B ARG* 3.1 13.5 - - + +
439B ILE* 2.9 37.6 + - + +
440B ILE 4.2 0.9 + - - -
119M LYS* 5.5 3.4 - - - +
120M GLU* 6.0 1.6 - - - -
123M THR* 4.1 31.9 - - + +
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Residues in contact with THR 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 3.3 47.4 - - + +
149B ILE* 3.2 25.4 - - - +
150B GLY* 4.3 2.0 - - - -
435B ILE* 3.7 7.3 + - + +
436B LYS* 1.3 71.2 - - - +
438B ARG* 1.3 61.2 + - - +
439B ILE 3.1 0.7 + - - -
440B ILE 3.4 2.9 + - - -
441B SER* 3.2 23.4 + - - -
123M THR* 5.3 1.5 + - - +
126M ASP* 2.4 36.5 + - - +
127M ARG* 4.8 10.0 + - + +
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Residues in contact with ARG 438 (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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436B LYS* 3.1 8.8 - - + +
437B THR* 1.3 83.0 + - - +
439B ILE* 1.3 80.7 - - - +
441B SER* 3.9 3.6 - - - -
442B ASP* 2.9 40.0 + - + +
119M LYS* 3.1 37.4 - - - +
122M THR* 3.8 28.6 + - - +
123M THR* 4.5 14.0 + - - +
126M ASP* 3.8 16.8 + - + +
61Y A 3.6 37.3 + - - -
62Y C 3.6 8.8 + - - -
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Residues in contact with ILE 439 (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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407B MET* 4.0 25.5 - - - +
410B ASN* 4.5 17.7 - - + +
411B LEU* 4.3 24.0 - - + +
414B GLU* 4.8 15.3 - - + +
436B LYS* 2.9 34.3 + - + +
438B ARG* 1.3 95.9 - - - +
440B ILE* 1.3 62.3 + - - +
443B GLY* 3.1 21.3 + - - -
119M LYS* 5.0 3.6 - - - +
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.0 3.1 - - + -
149B ILE* 3.8 25.8 - - + +
150B GLY* 4.2 7.6 - - - -
152B ILE* 3.9 17.3 - - + -
404B PHE* 3.9 30.3 - - + -
407B MET* 3.6 40.6 - - + +
408B PHE* 4.0 7.0 - - + +
411B LEU* 4.0 25.4 - - + -
436B LYS 5.3 0.2 - - - +
437B THR 3.4 1.4 + - - -
439B ILE* 1.3 74.5 - - + +
441B SER* 1.3 68.7 + - - +
444B LEU* 3.3 24.7 + - + +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY* 3.1 8.5 - - - -
151B LYS* 2.4 69.9 + - - +
153B PRO* 5.5 0.3 - - - +
437B THR* 3.2 11.3 + - - -
438B ARG* 4.3 4.5 - - - -
440B ILE* 1.3 77.1 - - - +
442B ASP* 1.3 62.6 + - - +
444B LEU* 4.2 0.7 - - - +
445B LYS* 3.2 25.9 + - - +
126M ASP* 5.1 1.1 + - - -
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Residues in contact with ASP 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ARG* 2.9 29.9 + - + +
441B SER* 1.3 79.4 - - - +
443B GLY* 1.3 59.3 + - - +
445B LYS* 3.9 26.6 + - - +
446B TYR* 2.8 32.2 + - - +
60Y A 2.9 37.9 + - - +
61Y A 3.0 17.8 + - - +
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B MET* 3.4 28.5 - - - +
439B ILE 3.1 14.0 + - - -
441B SER 3.4 0.2 - - - -
442B ASP* 1.3 78.3 - - - +
444B LEU* 1.3 58.3 + - - +
446B TYR* 3.7 5.9 + - - +
447B SER* 3.1 25.6 + - - -
455B ASP* 5.9 2.9 - - - -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 5.7 3.1 - - + -
151B LYS 5.4 0.2 - - - +
152B ILE* 3.5 34.3 - - + -
153B PRO* 4.3 17.9 - - + -
400B LEU* 3.9 22.2 - - + +
403B LEU* 3.6 33.9 - - + -
404B PHE* 4.2 19.5 - - + +
407B MET* 3.8 10.0 - - + -
440B ILE* 3.3 16.9 + - + +
441B SER 4.2 1.8 - - - +
443B GLY* 1.3 72.2 - - - +
445B LYS* 1.3 66.9 + - - +
446B TYR 3.2 0.2 - - - -
447B SER* 3.1 4.7 + - - +
448B LEU* 3.0 30.4 + - + +
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Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR* 4.0 17.3 - - + +
153B PRO* 4.8 11.1 - - + +
187B ILE* 3.9 18.3 - - + +
188B ASN* 3.7 18.6 + - - +
441B SER* 3.2 19.8 + - - +
442B ASP* 3.8 18.4 + - - +
444B LEU* 1.3 77.6 - - - +
446B TYR* 1.3 62.8 + - - +
448B LEU* 3.6 3.6 + - - +
449B ALA* 3.1 26.0 + - - +
913B GLN* 3.1 27.3 + - - -
60Y A 3.1 26.8 + - - +
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ASP* 2.8 25.2 + - - +
443B GLY* 3.8 5.8 - - - +
445B LYS* 1.3 77.7 - - - +
447B SER* 1.3 70.3 + - - +
449B ALA* 3.3 4.5 + - + +
450B THR* 2.9 53.8 + - + +
452B ASN* 3.0 32.7 + - + -
454B GLY 5.0 6.7 - - - -
455B ASP* 5.7 2.9 - - - -
456B GLN* 3.7 25.5 + - + +
59Y G 5.8 1.6 - + + -
60Y A 3.5 51.4 - + + -
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 3.6 34.7 - - - +
407B MET* 4.2 0.5 - - - +
443B GLY 3.1 13.1 + - - -
444B LEU 3.1 6.0 + - - -
446B TYR* 1.3 81.3 - - - +
448B LEU* 1.3 64.1 + - - +
450B THR* 3.7 3.8 + - - -
451B GLY* 3.1 24.9 + - - -
452B ASN 3.8 16.4 - - - +
453B TRP* 5.2 2.2 - - - -
454B GLY 3.8 18.2 + - - -
467B SER* 4.4 2.6 - - - -
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 3.6 38.8 - - + -
185B PHE* 4.0 30.7 - - + -
187B ILE* 3.6 21.3 - - + -
192B LYS* 3.0 16.5 - - + +
194B LEU* 5.2 9.0 - - + -
400B LEU* 4.2 24.5 - - + -
403B LEU* 4.8 2.7 - - + -
444B LEU* 3.0 20.2 + - + +
445B LYS 4.0 1.3 - - - +
447B SER* 1.3 83.4 - - - +
449B ALA* 1.3 58.4 + - - +
453B TRP* 6.5 0.2 - - + -
467B SER* 2.8 28.1 + - - +
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Residues in contact with ALA 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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187B ILE* 4.1 19.5 - - + +
188B ASN* 4.2 12.6 - - - +
192B LYS* 3.0 27.6 + - - +
445B LYS* 3.1 19.5 + - + +
446B TYR* 3.8 3.4 - - - +
448B LEU* 1.3 77.9 - - - +
450B THR* 1.3 61.2 + - + +
60Y A 4.6 7.9 - - - +
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Residues in contact with THR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 4.8 4.1 + - - -
446B TYR* 2.9 48.5 + - + +
447B SER* 3.7 0.9 + - - -
449B ALA* 1.3 83.0 - - + +
451B GLY* 1.3 63.5 + - - +
452B ASN* 3.2 30.0 + - - +
61M THR* 3.7 24.5 - - - +
59Y G 6.0 9.9 - - + +
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Residues in contact with GLY 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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192B LYS* 5.4 0.2 - - - -
447B SER 3.1 10.9 + - - -
448B LEU 4.2 0.6 + - - -
449B ALA 3.5 1.6 - - - -
450B THR* 1.3 77.9 + - - +
452B ASN* 1.3 67.3 + - - +
463B ARG 3.6 14.9 - - - +
465B GLY* 3.7 14.1 + - - -
466B VAL* 4.1 5.7 - - - +
467B SER* 3.8 27.6 - - - -
61M THR* 5.7 0.7 - - - -
62M LYS* 4.2 4.4 + - - -
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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
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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