Contacts of the helix formed by residues 538 - 549 (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 PRO 538 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B SER 3.3 7.2 - - - +
537B GLN* 1.3 85.7 - - + +
539B SER* 1.3 66.1 + - - +
540B PRO* 3.5 0.9 - - - -
541B ILE* 3.2 11.7 + - + +
542B LEU* 3.1 32.1 + - + +
569B VAL* 4.1 18.3 - - + +
570B ASN* 4.3 8.1 - - - +
616B THR* 3.6 24.7 - - + -
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Residues in contact with SER 539 (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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537B GLN* 3.4 26.4 + - - +
538B PRO* 1.3 77.2 - - - +
540B PRO* 1.4 67.6 - - - +
542B LEU* 3.3 13.0 + - - +
543B GLU* 2.9 37.7 + - - +
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Residues in contact with PRO 540 (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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537B GLN* 3.4 18.6 - - + +
538B PRO 3.6 0.4 - - - -
539B SER* 1.4 97.9 - - - +
541B ILE* 1.3 61.0 + - + +
543B GLU* 3.2 12.0 + - + +
544B PHE* 3.0 29.5 + - - +
595B ASP 5.9 2.9 - - - +
596B ILE* 6.3 1.6 - - + -
597B ILE* 6.1 7.0 - - + -
132T ILE* 4.5 29.0 - - + +
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Residues in contact with ILE 541 (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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537B GLN 5.4 0.9 - - - +
538B PRO* 3.2 11.7 + - + +
540B PRO* 1.3 81.0 - - + +
542B LEU* 1.3 63.7 + - + +
544B PHE* 3.4 5.0 + - - +
545B LEU* 3.2 42.0 + - + +
569B VAL* 5.0 10.1 - - + -
587B LEU* 5.2 3.1 - - + -
596B ILE* 4.4 25.8 - - + -
601B VAL* 3.7 39.0 - - + -
614B ILE* 4.4 21.3 - - + -
616B THR* 4.3 18.4 - - + +
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Residues in contact with LEU 542 (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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538B PRO* 3.1 34.1 + - + +
539B SER* 3.5 9.6 - - - +
541B ILE* 1.3 76.0 - - - +
543B GLU* 1.3 63.7 + - + +
545B LEU* 4.1 5.8 - - + +
546B GLU* 3.3 25.9 + - - +
550B MET* 5.2 4.8 - - + +
569B VAL* 3.7 35.4 - - + -
574B VAL* 3.7 21.8 - - + -
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Residues in contact with GLU 543 (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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539B SER* 2.9 22.9 + - - +
540B PRO* 3.4 14.4 - - + +
541B ILE 3.2 0.4 - - - -
542B LEU* 1.3 77.2 - - - +
544B PHE* 1.3 64.4 + - - +
546B GLU* 3.3 5.7 + - - +
547B GLU* 3.1 11.2 + - - +
121S ASN* 2.7 46.4 + - + +
128T LYS* 4.4 10.4 + - - -
131T GLN* 5.3 4.9 - - - +
132T ILE* 4.6 16.5 - - + +
135T SER* 4.4 18.6 + - - -
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Residues in contact with PHE 544 (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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540B PRO 3.0 15.7 + - - +
541B ILE* 3.4 5.1 + - - +
543B GLU* 1.3 77.2 - - - +
545B LEU* 1.3 69.0 + - + +
547B GLU* 3.1 22.5 - - - +
548B TRP* 3.0 69.3 + + - +
583B LEU* 4.6 4.3 - - + -
586B THR* 4.1 9.0 - - + -
587B LEU* 3.8 28.7 - - + -
590B LEU* 3.3 33.4 - - + -
596B ILE* 5.1 4.7 - - + -
125T MET* 4.2 22.2 - - + -
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Residues in contact with LEU 545 (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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541B ILE* 3.2 33.0 + - + +
542B LEU* 4.1 5.2 - - - +
544B PHE* 1.3 84.4 - - + +
546B GLU* 1.3 62.3 + - - +
548B TRP* 3.2 11.8 + - - +
549B SER 3.3 1.6 + - - -
550B MET* 3.3 41.0 + - + +
567B ILE* 4.2 25.1 - - + -
569B VAL* 4.5 8.7 - - + -
574B VAL* 5.4 0.2 - - + -
583B LEU* 3.9 36.6 - - + -
587B LEU* 4.2 13.9 - - + -
614B ILE* 4.2 9.2 - - + -
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Residues in contact with GLU 546 (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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542B LEU 3.3 18.0 + - - +
543B GLU* 3.3 6.0 + - - +
545B LEU* 1.3 80.4 - - - +
547B GLU* 1.3 58.0 + - - +
548B TRP 3.7 0.2 + - - -
549B SER* 4.5 1.9 + - - -
550B MET* 4.3 24.6 - - + +
552B ASN* 6.3 2.9 - - + -
118S VAL 4.5 10.7 - - - +
119S THR* 4.8 1.9 - - - +
120S GLU* 5.3 0.9 + - - +
121S ASN* 3.5 26.2 + - - +
122S THR* 3.8 33.1 + - + +
22T LYS* 5.2 6.9 + - - +
115T GLU* 4.7 5.9 - - - +
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Residues in contact with GLU 547 (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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543B GLU* 3.1 10.1 + - - +
544B PHE* 3.1 40.7 + - + +
546B GLU* 1.3 75.3 - - - +
548B TRP* 1.3 69.5 + - + +
121S ASN* 3.4 17.5 + - - +
122S THR* 5.0 4.9 - - - -
24T PRO* 6.1 6.5 - - + +
115T GLU* 4.1 8.4 - - - +
117T ARG* 4.8 1.9 + - - +
118T PRO* 5.2 11.8 - - - +
124T TYR* 3.2 34.8 + - - +
125T MET* 5.2 3.8 - - - +
128T LYS* 3.2 31.3 + - - +
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Residues in contact with TRP 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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544B PHE* 3.0 51.7 + + + +
545B LEU* 3.2 8.7 + - - +
547B GLU* 1.3 82.3 - - + +
549B SER* 1.3 87.0 + - - +
577B HIS* 4.7 4.5 - + - -
579B ASP* 6.4 0.2 - - + -
582B GLN* 4.8 8.5 - - + -
583B LEU* 3.8 30.5 - - + -
586B THR* 3.6 35.4 - - + +
115T GLU* 4.2 1.2 - - - +
117T ARG* 2.5 52.2 + - - +
125T MET* 4.9 9.3 - - + +
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Residues in contact with SER 549 (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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545B LEU 3.3 0.2 + - - -
546B GLU 4.5 1.3 + - - -
547B GLU 3.7 1.2 - - - -
548B TRP* 1.3 100.1 - - - +
550B MET* 1.3 67.4 + - - +
551B GLU* 3.3 12.1 + - - +
576B ILE 5.0 0.2 - - - +
577B HIS* 2.4 38.6 + - - -
583B LEU* 4.8 1.2 - - - +
115T GLU* 4.4 16.8 - - - +
117T ARG* 4.2 7.2 - - - +
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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