Contacts of the helix formed by residues 257 - 267 (chain B) in PDB entry 5CYO
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 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ARG* 4.0 18.1 + - - +
183B LYS* 2.8 35.6 + - - +
219B MET* 3.8 18.5 - - - +
222B PHE* 3.6 11.8 - - + -
223B ALA* 2.8 33.4 + - - +
224B VAL* 4.9 1.3 - - - -
253B THR 5.4 1.6 - - - +
256B CYS* 1.3 77.3 - - - +
258B PHE* 1.3 64.7 + - - +
259B ALA 3.3 2.5 - - - -
260B TYR* 3.3 25.6 + - + +
261B LEU* 3.1 20.7 + - - +
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Residues in contact with PHE 258 (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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39B LEU* 3.9 29.6 - - + -
42B THR* 3.7 25.6 - - + -
43B LEU* 3.8 35.2 - - + -
46B SER* 4.1 19.7 - - - -
223B ALA 3.8 2.0 + - - -
224B VAL* 4.4 11.2 - - + -
225B VAL 4.4 2.9 - - - +
250B VAL* 3.6 33.4 - - + +
251B GLU* 4.3 7.9 - - + -
256B CYS* 3.5 11.3 - - - -
257B GLU* 1.3 78.1 - - - +
259B ALA* 1.3 61.5 + - - +
261B LEU* 3.1 10.6 + - + +
262B ARG* 2.8 39.5 + - + +
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Residues in contact with ALA 259 (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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250B VAL 4.2 2.2 + - - -
251B GLU* 3.6 28.7 - - - +
253B THR* 3.9 21.1 - - + +
256B CYS 4.9 0.4 + - - -
257B GLU 3.3 0.8 - - - -
258B PHE* 1.3 82.7 - - - +
260B TYR* 1.3 62.1 + - - +
262B ARG* 3.8 21.3 - - - +
263B ASP* 3.1 31.6 + - - +
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Residues in contact with TYR 260 (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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219B MET* 3.7 42.0 - - + -
222B PHE* 4.5 0.9 - - + -
253B THR* 3.5 47.3 + - + +
256B CYS 4.7 0.9 - - - -
257B GLU* 3.3 26.3 + - + +
258B PHE 3.2 0.2 - - - -
259B ALA* 1.3 76.8 - - - +
261B LEU* 1.3 57.9 + - - +
263B ASP* 3.4 3.1 + - - +
264B LEU* 2.8 38.9 + - + +
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Residues in contact with LEU 261 (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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39B LEU* 4.9 5.2 - - + -
137B LEU* 4.2 16.6 - - + -
165B VAL* 4.1 12.1 - - + -
167B VAL* 3.7 26.2 - - + -
216B PHE* 5.1 0.7 - - + -
222B PHE* 3.9 35.8 - - + -
224B VAL* 3.8 13.7 - - + -
257B GLU 3.1 9.2 + - - +
258B PHE* 3.1 13.8 + - + +
260B TYR* 1.3 76.6 - - - +
262B ARG* 1.3 65.9 + - - +
264B LEU* 3.4 1.1 + - - -
265B LEU* 3.0 60.0 + - + +
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Residues in contact with ARG 262 (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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43B LEU* 3.8 24.2 - - + -
46B SER* 3.3 20.5 + - - -
47B LYS* 4.4 17.5 - - + +
251B GLU* 2.6 42.4 + - - +
258B PHE* 2.8 34.2 + - + +
259B ALA* 3.8 20.0 + - - +
261B LEU* 1.3 74.3 - - - +
263B ASP* 1.3 95.6 + - - +
265B LEU* 5.1 2.2 - - - -
266B ILE* 3.0 41.9 + - + +
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Residues in contact with ASP 263 (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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47B LYS* 5.0 4.5 + - - -
259B ALA 3.1 11.5 + - - +
260B TYR* 4.1 2.9 - - - +
262B ARG* 1.3 117.9 + - - +
264B LEU* 1.3 64.7 + - + +
266B ILE* 4.2 9.4 - - - +
267B ARG* 3.1 30.9 + - + +
268B THR* 3.3 9.3 + - + +
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Residues in contact with LEU 264 (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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212B VAL* 6.3 0.2 - - + -
215B LYS* 6.4 1.1 - - + -
216B PHE* 3.7 31.0 - - + +
219B MET* 3.7 30.1 - - + -
222B PHE* 3.8 14.6 - - + -
260B TYR* 2.8 24.4 + - + +
261B LEU* 3.9 3.6 - - - +
263B ASP* 1.3 77.6 - - + +
265B LEU* 1.3 61.7 + - - +
268B THR* 3.2 21.5 - - + +
269B HIS* 2.9 51.4 + - + +
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Residues in contact with LEU 265 (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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24B PHE* 3.3 23.4 - - + -
26B ILE* 4.4 14.6 - - + -
43B LEU* 6.0 2.5 - - + -
135B CYS* 4.1 17.3 - - + -
137B LEU* 3.8 24.0 - - + -
165B VAL* 4.3 2.5 - - + -
216B PHE* 4.1 22.0 - - + -
261B LEU* 3.0 43.1 + - + +
262B ARG* 4.2 3.4 - - - +
264B LEU* 1.3 79.5 - - - +
266B ILE* 1.3 62.9 + - + +
270B MET* 3.3 18.2 - - - +
273B ILE* 3.8 21.5 - - + +
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Residues in contact with ILE 266 (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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24B PHE* 5.0 10.3 - - + -
26B ILE* 5.1 5.4 - - + -
43B LEU* 5.0 12.6 - - + -
47B LYS* 3.4 38.8 - - + +
74B ILE* 4.9 11.2 - - + -
81B MET* 3.6 22.8 - - + +
83B LEU* 5.1 6.1 - - + -
262B ARG* 3.0 33.1 + - + +
263B ASP* 4.2 7.2 - - - +
265B LEU* 1.3 84.3 - - + +
267B ARG* 1.3 65.9 + - + +
270B MET* 3.5 18.9 - - - +
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Residues in contact with ARG 267 (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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263B ASP* 3.1 20.3 + - + +
265B LEU 3.6 0.4 - - - -
266B ILE* 1.3 86.1 - - + +
268B THR* 1.3 72.0 + - + +
269B HIS 3.6 0.8 + - - -
270B MET* 4.0 9.4 + - - +
271B GLN 5.1 1.2 + - - -
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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