Contacts of the helix formed by residues 265 - 274 (chain D) in PDB entry 2IYL
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 VAL 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ASP* 3.3 26.7 + - + +
230D ALA* 4.3 32.8 - - + +
233D GLY* 5.1 10.1 - - - +
257D LEU* 4.4 7.0 - - + -
261D ALA* 4.6 9.4 - - + -
262D LYS 3.5 19.2 + - - +
263D GLY 4.1 3.4 - - - +
264D GLY* 1.3 75.7 - - - +
266D LEU* 1.3 68.2 + - + +
267D ILE 3.1 0.2 - - - -
268D PRO* 3.2 17.7 - - + +
269D ILE* 3.3 24.4 - - + +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 3.8 13.4 - - + +
254D VAL* 3.7 41.7 - - + -
257D LEU* 3.9 16.4 - - + -
263D GLY 3.3 10.3 - - - +
264D GLY 3.1 1.0 - - - -
265D VAL* 1.3 79.0 - - + +
267D ILE* 1.3 65.5 + - - +
269D ILE* 3.4 6.3 + - - +
270D VAL* 3.1 25.6 + - - +
277D ILE* 4.4 9.0 - - + -
280D VAL* 4.2 11.9 - - + -
292D PHE* 3.4 34.1 - - + -
297D PHE* 3.7 18.4 - - + -
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Residues in contact with ILE 267 (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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44D VAL* 4.1 10.8 - - + -
48D ALA* 3.8 12.6 - - + -
72D LEU* 3.3 37.2 - - + -
75D MET* 3.2 42.2 - - + +
76D LEU* 4.4 11.4 - - + -
264D GLY 3.1 9.6 + - - +
265D VAL 3.1 1.0 - - - -
266D LEU* 1.3 81.1 - - - +
268D PRO* 1.3 70.6 - - + +
270D VAL* 3.2 1.7 + - - +
271D ARG* 3.0 20.6 + - - +
297D PHE* 4.2 17.5 - - + -
301D LEU* 4.3 13.2 - - + -
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Residues in contact with PRO 268 (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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43D ASP 4.4 3.6 - - - +
44D VAL 3.5 21.1 - - - +
45D GLY* 5.5 1.8 - - - -
48D ALA* 5.3 1.8 - - + -
237D LEU* 4.5 8.1 - - + -
264D GLY 3.4 8.7 - - - +
265D VAL* 3.2 25.4 - - + +
267D ILE* 1.3 88.4 - - + +
269D ILE* 1.3 58.8 + - + +
271D ARG* 4.1 13.0 - - + +
272D THR* 2.7 35.9 + - - +
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Residues in contact with ILE 269 (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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228D LEU* 3.8 27.8 - - + -
229D ASP 5.1 4.3 - - - +
233D GLY* 5.1 10.5 - - - +
237D LEU* 4.2 18.8 - - + +
252D VAL* 4.4 5.6 - - + -
254D VAL* 3.9 32.1 - - + -
265D VAL* 3.3 24.4 + - + +
266D LEU* 3.6 9.6 - - - +
267D ILE 3.1 1.0 - - - -
268D PRO* 1.3 78.7 - - + +
270D VAL* 1.3 59.7 + - + +
272D THR* 3.8 0.5 - - - -
273D LEU* 2.9 39.8 + - + +
277D ILE* 4.1 17.0 - - + -
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Residues in contact with VAL 270 (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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75D MET 3.1 23.3 - - - +
76D LEU* 3.8 14.1 - - + +
78D PRO* 3.6 30.1 - - + +
266D LEU 3.1 12.3 + - - +
267D ILE 4.1 1.1 - - - +
269D ILE* 1.3 74.2 - - + +
271D ARG* 1.3 60.3 + - - +
274D LYS* 2.8 28.4 + - - +
275D VAL 3.6 19.5 - - - +
277D ILE* 3.6 38.6 - - + +
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Residues in contact with ARG 271 (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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47D SER* 4.0 15.8 + - - -
48D ALA* 3.5 21.9 - - - +
51D GLU* 3.3 41.5 + - - +
75D MET* 2.8 52.4 + - + +
267D ILE 3.0 15.6 + - - +
268D PRO* 3.6 9.0 - - + +
270D VAL* 1.3 77.5 - - - +
272D THR* 1.3 62.5 + - - +
274D LYS* 3.7 19.1 - - - +
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Residues in contact with THR 272 (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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237D LEU* 3.6 36.8 - - + +
241D LYS* 3.5 38.3 + - + -
268D PRO* 2.7 23.2 + - - +
269D ILE 3.8 2.2 - - - -
271D ARG* 1.3 82.0 - - - +
273D LEU* 1.3 60.8 + - + +
274D LYS* 4.2 7.7 - - - +
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Residues in contact with LEU 273 (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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226D LEU* 3.8 26.0 - - + -
228D LEU* 3.9 15.9 - - + -
237D LEU* 3.9 13.5 - - + +
240D ALA* 3.8 21.8 - - + +
241D LYS* 3.9 26.2 - - + +
244D HIS* 5.0 16.3 + - + -
249D LEU* 4.6 8.6 - - + +
252D VAL* 3.9 15.7 - - + -
269D ILE* 2.9 17.8 + - + +
270D VAL* 4.9 0.7 - - - -
272D THR* 1.3 77.3 - - + +
274D LYS* 1.3 73.0 + - - +
275D VAL* 3.3 20.5 + - + +
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Residues in contact with LYS 274 (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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78D PRO* 3.5 26.6 - - + +
79D ASP* 4.8 4.5 - - - +
241D LYS* 5.6 5.6 - - - +
270D VAL 2.8 17.5 + - - +
271D ARG* 3.7 19.5 - - - +
272D THR 4.2 6.3 - - - +
273D LEU* 1.3 81.8 - - - +
275D VAL* 1.3 62.3 + - - +
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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