Contacts of the helix formed by residues 253 - 261 (chain F) in PDB entry 6R7H
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 ASN 253 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245F SER* 5.8 2.5 - - - -
250F VAL* 5.8 0.7 - - - -
251F PRO* 3.1 24.2 + - - +
252F PHE* 1.3 86.3 - - - +
254F HIS* 1.3 65.1 + - - +
255F GLU* 3.5 6.9 + - + +
256F ILE* 3.7 29.9 + - + +
257F LEU* 3.7 25.8 + - - +
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Residues in contact with HIS 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F PHE* 5.2 7.9 - + + -
253F ASN* 1.3 72.8 - - - +
255F GLU* 1.3 71.4 + - + +
256F ILE 3.4 0.2 - - - -
257F LEU* 4.1 7.4 - - - +
258F ARG* 3.3 28.6 + - - +
9G SER 6.1 0.4 - - - -
12G LEU* 4.7 28.8 - - + +
13G GLU* 4.8 14.6 - - + +
16G ILE* 4.5 18.6 - - + +
42G VAL* 5.9 5.6 - - + +
45G GLU* 4.8 22.1 + - + +
162G ILE* 4.2 27.8 - - + -
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Residues in contact with GLU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D LYS* 5.6 3.6 - - - +
253F ASN* 3.3 5.9 - - + +
254F HIS* 1.3 88.1 + - + +
256F ILE* 1.3 66.9 - - + +
258F ARG* 2.6 45.2 + - - +
259F GLU* 3.3 53.6 + - - +
9G SER* 3.3 21.1 + - - +
12G LEU* 4.7 3.8 - - - +
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Residues in contact with ILE 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LYS* 4.4 11.9 - - - +
241F TYR* 3.4 45.8 - - + +
242F VAL* 5.8 4.7 - - + -
245F SER* 4.1 16.4 - - - +
250F VAL* 4.3 21.5 - - + -
253F ASN* 3.7 30.8 + - + +
254F HIS 3.4 0.4 - - - -
255F GLU* 1.3 76.8 - - + +
257F LEU* 1.3 67.5 + - + +
259F GLU* 3.4 6.5 + - - +
260F ALA* 3.2 26.8 + - + +
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F VAL* 5.1 14.6 - - + +
245F SER* 4.8 21.3 - - - +
246F GLU* 5.8 1.1 - - + +
252F PHE* 3.6 33.7 - - + -
253F ASN 3.7 16.0 + - - +
254F HIS* 3.8 4.9 + - - +
255F GLU 3.4 0.4 - - - -
256F ILE* 1.3 79.2 - - + +
258F ARG* 1.3 61.3 + - - +
260F ALA* 4.0 1.5 - - - -
261F TYR* 3.3 28.1 + - - +
162G ILE* 3.5 28.5 - - + +
163G ARG* 5.1 6.3 - - + +
167G ILE* 4.0 29.4 - - + -
170G ILE* 4.7 6.9 - - + +
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Residues in contact with ARG 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F HIS* 3.3 16.4 + - - +
255F GLU* 2.6 39.1 + - - +
257F LEU* 1.3 78.2 - - - +
259F GLU* 1.3 58.4 + - + +
260F ALA 3.6 0.2 - - - -
261F TYR* 4.4 8.7 + - - +
262F ALA 5.2 0.9 + - - -
8G SER 3.5 11.9 + - - +
9G SER* 2.9 27.9 + - - -
12G LEU* 3.4 24.2 - - - +
39G GLY 5.5 1.8 + - - -
41G TYR* 5.5 6.5 - - - +
42G VAL* 4.4 25.4 - - + +
156G PHE* 4.5 9.9 - - - -
157G CYS 4.8 7.1 - - - +
158G ILE* 4.5 27.3 - - + +
159G GLY* 5.0 8.6 + - - +
161G ASP 5.2 6.3 - - - +
162G ILE* 6.4 0.4 - - - -
163G ARG* 6.1 1.1 - - - -
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Residues in contact with GLU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D LEU* 5.7 8.5 - - + +
387D LYS* 4.0 29.3 + - - +
255F GLU* 3.3 46.1 + - - +
256F ILE* 3.4 4.8 + - - +
257F LEU 3.2 0.4 - - - -
258F ARG* 1.3 81.9 - - + +
260F ALA* 1.3 58.1 + - - +
261F TYR 3.6 1.3 - - - -
263F LEU* 4.2 6.6 - - - +
156G PHE* 4.0 25.8 - - + -
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Residues in contact with ALA 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D LEU* 5.6 6.3 - - + -
241F TYR* 6.2 1.8 - - + -
242F VAL* 4.4 29.8 - - + -
256F ILE* 3.2 18.2 + - + +
257F LEU* 4.0 2.0 - - - +
258F ARG 3.6 0.2 - - - -
259F GLU* 1.3 77.7 - - - +
261F TYR* 1.3 64.4 + - - +
262F ALA 3.6 0.7 - - - -
263F LEU* 3.9 24.4 + - + +
264F CYS* 4.4 6.6 + - - -
170G ILE* 3.9 16.5 - - + +
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Residues in contact with TYR 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F LEU 3.3 17.8 + - - +
258F ARG* 4.8 6.1 - - - +
259F GLU 3.6 1.0 - - - +
260F ALA* 1.3 80.3 - - - +
262F ALA* 1.3 70.5 + - + +
263F LEU 3.2 1.4 + - - -
264F CYS* 4.1 3.1 + - - +
265F HIS* 4.0 26.8 + + - +
106G SER* 3.5 31.8 + - - -
157G CYS* 4.9 6.1 - - - -
158G ILE 4.5 5.4 - - - -
159G GLY* 3.8 15.5 - - - -
163G ARG* 3.3 49.5 + - + -
166G ASP* 4.0 20.5 + - + +
169G ASN* 5.7 6.3 - - + -
170G ILE* 3.7 29.5 - - + +
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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