Contacts of the strand formed by residues 256 - 264 (chain A) in PDB entry 1YPN
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 GLU 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLU 3.4 0.2 - - - +
252A LEU* 3.5 5.9 - - - +
253A ILE* 2.8 40.8 + - - +
254A ASP* 4.3 9.2 - - - +
255A GLY* 1.3 84.4 - - - +
257A ILE* 1.3 63.7 + - - +
258A TRP 3.5 0.3 + - - -
277A ARG* 3.9 31.7 - - + +
278A GLY* 3.4 23.4 - - - +
279A ALA* 4.7 2.0 - - - +
280A PRO* 4.4 1.1 - - - -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 4.0 25.4 - - + -
227A ARG* 4.1 5.2 - - + +
230A ALA* 4.1 10.5 - - + -
250A ALA* 4.0 20.9 - - + -
251A GLU 3.4 4.0 - - - +
252A LEU* 3.5 31.2 - - + -
256A GLU* 1.3 70.8 - - - +
258A TRP* 1.3 61.8 + - - +
259A LEU* 4.2 1.3 - - + +
276A ARG 3.7 0.7 - - - +
277A ARG* 3.2 7.2 - - - +
278A GLY 2.9 27.3 + - - -
280A PRO* 4.0 24.5 - - + -
283A ALA* 4.8 6.1 - - + -
286A MET* 3.7 26.7 - - + +
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Residues in contact with TRP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLU* 5.1 2.2 - - - -
249A TYR 3.9 1.9 - - - +
250A ALA* 3.3 2.9 - - - -
251A GLU* 2.8 38.7 + - + +
253A ILE* 4.0 31.2 - - + -
256A GLU 3.5 0.6 + - - -
257A ILE* 1.3 74.1 - - - +
259A LEU* 1.3 59.2 + - - +
260A ARG* 3.5 56.3 + - + +
275A GLU* 2.9 36.0 + - - +
276A ARG 3.4 14.8 - - - -
277A ARG* 3.6 37.8 - - + +
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ALA* 3.9 9.0 - - + +
231A GLU* 4.1 18.8 - - + +
234A MET* 4.3 4.3 - - + -
248A SER* 4.2 4.5 - - - +
249A TYR 3.8 10.3 - - - +
250A ALA* 3.9 13.9 - - + -
257A ILE* 3.7 7.0 - - + -
258A TRP* 1.3 74.3 - - - +
260A ARG* 1.3 76.3 + - - +
275A GLU* 3.1 6.6 - - - +
276A ARG* 2.8 43.3 + - + +
286A MET* 4.3 17.3 - - + +
287A GLY* 3.5 33.9 - - - +
290A LEU* 3.7 20.4 - - + -
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Residues in contact with ARG 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PRO* 4.4 6.0 + - - +
190A GLU* 3.0 43.4 + - - +
193A LEU* 3.8 17.2 - - + +
248A SER* 3.5 1.0 - - - -
249A TYR* 3.0 59.4 + - - +
251A GLU* 3.9 16.0 + - - +
258A TRP* 3.5 55.2 + - + -
259A LEU* 1.3 81.9 - - - +
261A ALA* 1.3 64.6 + - - +
274A GLY 3.6 5.6 - - - +
275A GLU* 4.1 10.5 - - + +
290A LEU* 4.2 1.1 - - - -
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 3.6 7.3 - - - +
234A MET* 3.6 25.6 - - + -
247A GLY 3.2 15.0 - - - +
248A SER* 4.4 0.4 - - - -
260A ARG* 1.3 79.0 - - - +
262A LEU* 1.3 64.3 + - - +
273A ARG* 3.5 3.1 - - - +
274A GLY 3.1 29.2 + - - +
290A LEU* 3.7 18.6 - - + -
294A LEU* 4.2 8.3 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 5.3 1.1 - - + +
134A CYS* 4.2 17.9 - - - -
135A GLN* 3.4 32.8 - - + +
193A LEU* 4.4 9.6 - - + -
234A MET* 5.2 0.2 - - - +
245A PRO 4.4 1.8 - - - +
246A ILE* 3.4 4.0 - - - +
247A GLY* 2.9 42.0 + - - +
261A ALA* 1.3 79.0 - - - +
263A VAL* 1.3 76.7 + - - +
264A GLY 4.1 4.9 - - - +
271A ILE* 4.0 24.2 - - + -
272A ILE 3.0 14.4 - - - +
273A ARG* 4.2 20.0 - - + +
294A LEU* 4.0 1.3 - - - -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LEU* 3.8 28.5 - - + -
245A PRO* 3.2 9.2 - - + +
246A ILE* 4.0 5.4 - - + -
262A LEU* 1.3 81.9 - - - +
264A GLY* 1.3 60.5 + - - +
270A GLN 4.2 0.2 - - - +
271A ILE* 3.6 0.2 - - - -
272A ILE* 2.8 34.7 + - + +
294A LEU* 3.8 13.5 - - + -
299A ALA* 4.1 22.7 - - + -
302A ILE* 4.2 14.6 - - + +
303A LEU* 3.8 32.5 - - + -
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Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS* 4.1 6.7 - - - -
245A PRO* 3.0 39.2 + - - +
262A LEU* 4.1 4.0 - - - +
263A VAL* 1.3 75.8 - - - +
265A ALA* 1.3 63.6 + - - -
270A GLN 3.4 9.0 - - - -
271A ILE* 4.0 13.5 - - - -
302A ILE* 3.8 8.3 - - - +
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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