Contacts of the helix formed by residues 17 - 26 (chain 1) in PDB entry 5IY6
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 17 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131 ASP* 2.3 38.8 - - - +
141 PRO* 3.7 12.9 + - + -
161 MET* 1.3 87.4 - - + +
181 GLN* 1.3 53.8 + - - +
191 PHE 3.3 0.2 - - - -
201 LEU* 2.6 35.0 + - - +
211 LEU* 3.1 9.4 + - + +
514V MET* 4.7 10.8 - - - +
519V TYR* 3.3 34.7 + - + -
666V ASP* 2.9 51.8 + - - +
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Residues in contact with GLN 18 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 ASP* 3.6 3.8 + - + -
141 PRO 3.4 17.4 + - - +
151 ALA* 4.4 2.0 - - - -
171 LYS* 1.3 77.0 - - - +
191 PHE* 1.3 129.0 + - + +
211 LEU* 3.1 16.5 + - - +
221 TYR* 3.0 22.7 + - - +
381 ILE* 5.4 1.2 - - - +
411 THR* 2.9 33.9 + - - +
441 PHE* 2.8 43.0 - - + -
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Residues in contact with PHE 19 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ALA* 3.0 29.4 - - + -
161 MET 4.2 3.8 - - - +
171 LYS 3.3 0.4 - - - -
181 GLN* 1.3 118.9 + - + +
201 LEU* 1.3 55.6 + - - +
221 TYR* 3.2 10.3 + + + +
231 LEU* 2.8 36.0 + - - +
411 THR* 5.4 6.7 - - + -
516V PRO* 4.5 3.1 - - + -
517V GLU* 3.6 30.1 - - + -
520V ARG* 3.3 42.6 - - + -
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Residues in contact with LEU 20 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 MET 4.3 2.0 + - - +
171 LYS 2.6 20.0 + - - +
191 PHE* 1.3 70.8 - - - +
211 LEU* 1.3 72.3 + - + +
231 LEU* 3.2 11.8 + - + +
241 ASP* 2.8 27.8 + - + +
571 VAL* 6.1 0.9 - - + -
581 GLY* 4.7 15.0 - - - -
611 MET* 4.3 10.3 - - - -
519V TYR* 2.7 44.0 - - + +
520V ARG* 4.4 2.1 - - - +
523V VAL* 2.4 46.9 - - + -
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Residues in contact with LEU 21 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 GLU* 3.0 29.2 - - - +
131 ASP* 4.0 22.4 - - + +
171 LYS* 3.5 17.0 - - + +
181 GLN* 3.1 17.0 + - - +
201 LEU* 1.3 85.9 - - + +
221 TYR* 1.3 55.4 + - - +
241 ASP* 2.7 9.9 + - - +
251 GLU* 2.7 33.1 + - - +
351 ILE* 5.2 3.4 - - + -
441 PHE* 4.7 9.4 - - + -
461 ILE* 5.1 4.3 - - + -
541 GLN* 3.3 32.9 + - + +
581 GLY* 6.1 1.3 - - - -
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Residues in contact with TYR 22 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 GLN* 3.0 15.4 + - - +
191 PHE* 3.3 15.9 - + + +
211 LEU* 1.3 76.9 - - - +
231 LEU* 1.3 79.3 + - + +
251 GLU* 2.8 45.0 + - - +
261 SER* 3.0 22.2 + - - -
351 ILE* 4.3 15.7 - - + +
381 ILE* 5.6 6.5 - - + -
520V ARG* 6.1 1.3 - - - -
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Residues in contact with LEU 23 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 PHE 2.8 20.7 + - - +
201 LEU* 3.3 15.7 - - + +
221 TYR* 1.3 97.0 - - + +
241 ASP* 1.3 53.1 + - - +
261 SER* 2.5 32.0 - - - +
271 ASN* 4.3 12.5 - - + +
520V ARG* 3.2 54.7 - - + +
523V VAL* 5.4 1.1 - - + -
524V ALA* 3.8 17.9 - - + +
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Residues in contact with ASP 24 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 LEU* 2.8 16.4 + - + +
211 LEU* 2.7 17.8 + - - +
231 LEU* 1.3 78.1 - - - +
251 GLU* 1.3 59.4 + - - +
261 SER 3.0 7.1 - - - +
281 ALA* 3.1 12.4 - - - +
311 LYS* 3.3 26.3 + - - +
341 ILE* 4.1 0.7 - - - -
541 GLN* 2.5 26.8 - - - +
571 VAL* 2.7 35.8 - - - +
611 MET* 4.8 12.0 - - + +
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Residues in contact with GLU 25 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 LEU 2.7 13.7 + - - +
221 TYR* 2.8 26.9 + - - +
241 ASP* 1.3 77.1 - - - +
261 SER* 1.3 60.2 + - - -
281 ALA* 4.0 0.2 - - - +
311 LYS* 3.6 3.1 - - - +
321 LYS* 2.8 56.7 + - + +
341 ILE* 4.1 11.9 - - + -
351 ILE* 2.8 58.2 - - + +
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Residues in contact with SER 26 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 TYR* 3.0 30.7 + - - -
231 LEU* 2.5 22.8 - - - +
241 ASP 3.0 6.6 - - - +
251 GLU* 1.3 80.3 + - - +
271 ASN* 1.3 79.5 + - - +
281 ALA* 2.8 5.2 + - - +
321 LYS* 3.9 14.8 - - - +
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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