Contacts of the helix formed by residues 251 - 262 (chain A) in PDB entry 6VWW
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 LEU 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A ILE* 4.2 2.9 + - + +
237A VAL* 4.3 16.2 - - + +
249A LEU* 4.7 0.2 - - - +
250A HIS* 1.3 79.0 - - + +
252A LEU* 1.3 60.8 + - - +
253A ILE* 3.2 13.0 - - + -
254A GLY* 2.9 20.5 + - - +
255A LEU* 3.1 14.5 + - - +
295A VAL* 4.2 0.2 - - - -
296A ILE* 3.3 31.4 - - + +
298A LEU* 4.1 24.7 - - + +
300A LEU* 3.8 21.1 - - + -
303A PHE* 3.5 49.4 - - + -
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Residues in contact with LEU 252 (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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199A ARG 3.2 33.4 - - - +
200A ASN* 4.1 1.1 - - - +
201A LEU* 3.7 26.2 - - + +
204A PHE* 4.0 12.6 - - + -
251A LEU* 1.3 72.2 - - - +
253A ILE* 1.3 57.8 + - - +
255A LEU* 3.1 10.6 + - + +
256A ALA* 2.8 26.3 + - - +
279A TYR* 6.1 2.9 - - + -
295A VAL* 3.8 18.5 - - + +
296A ILE 3.1 9.0 + - - +
297A ASP* 3.4 40.5 - - + +
406A ACY 4.4 10.3 - - - +
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Residues in contact with ILE 253 (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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199A ARG* 5.4 1.1 - - - +
204A PHE* 3.5 31.8 - - + -
211A GLU* 3.7 47.8 - - + +
214A PHE* 3.5 35.3 - - + -
215A LEU* 4.1 5.8 - - + -
237A VAL* 4.6 1.8 - - + -
251A LEU* 4.1 24.0 - - + -
252A LEU* 1.3 78.1 - - - +
254A GLY* 1.3 59.1 + - - +
256A ALA* 3.6 1.9 - - - +
257A LYS* 3.0 23.0 + - - +
297A ASP* 5.0 1.0 + - - -
298A LEU 5.2 5.6 + - - +
300A LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 254 (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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214A PHE* 4.1 13.7 - - - -
237A VAL* 3.4 22.7 - - - -
238A TYR* 5.0 2.2 - - - +
249A LEU* 3.8 11.3 - - - +
251A LEU* 2.9 8.9 + - - +
253A ILE* 1.3 84.6 - - - +
255A LEU* 1.3 59.2 + - - +
257A LYS* 3.6 2.3 + - - +
258A ARG* 3.2 22.5 + - - +
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Residues in contact with LEU 255 (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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201A LEU* 3.6 12.8 - - + -
249A LEU* 3.7 43.3 - - + +
251A LEU 3.1 29.6 - - - +
252A LEU* 3.1 12.2 + - + +
254A GLY* 1.3 73.2 - - - +
256A ALA* 1.3 60.5 + - - +
258A ARG* 3.3 2.7 + - - -
259A PHE* 2.8 31.0 + - - +
264A PHE* 3.5 14.4 - - + -
266A LEU* 4.0 34.1 - - + -
279A TYR* 5.2 1.3 - - + -
281A ILE* 5.1 2.5 - - + -
293A CYS* 6.3 0.2 - - - -
295A VAL* 4.0 26.9 - - + -
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Residues in contact with ALA 256 (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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201A LEU* 3.4 15.5 - - + +
204A PHE* 3.6 40.8 - - + -
215A LEU* 4.9 4.3 - - + -
252A LEU 2.8 15.4 + - - +
253A ILE* 3.6 5.8 - - - +
254A GLY 3.3 0.4 - - - -
255A LEU* 1.3 77.2 - - - +
257A LYS* 1.3 63.4 + - - +
259A PHE* 3.2 12.2 + - - +
260A LYS* 3.3 13.7 + - - +
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Residues in contact with LYS 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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214A PHE* 2.9 40.7 + - + +
215A LEU* 2.8 44.8 + - + +
216A GLU 4.6 0.6 + - - -
217A LEU 3.1 16.2 + - - -
218A ALA* 5.2 2.9 - - - +
219A MET 5.4 0.7 - - - +
238A TYR* 4.2 19.7 - - + -
253A ILE 3.0 17.1 + - - +
254A GLY 4.0 3.6 - - - +
255A LEU 3.4 0.2 - - - -
256A ALA* 1.3 76.4 - - - +
258A ARG* 1.3 62.0 + - - +
260A LYS* 3.5 8.9 + - - +
261A GLU* 3.3 34.4 + - - +
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Residues in contact with ARG 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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238A TYR 5.5 1.3 - - - +
241A PHE* 3.8 42.8 - - + +
249A LEU* 5.2 3.8 - - + -
254A GLY 3.2 15.7 + - - +
255A LEU* 3.8 5.2 - - - +
256A ALA 3.3 0.2 - - - -
257A LYS* 1.3 78.7 - - - +
259A PHE* 1.3 59.3 + - - +
261A GLU* 3.1 23.4 + - - +
262A SER* 2.9 37.3 + - - +
264A PHE* 3.7 18.6 - - + -
283A ASP* 2.8 40.0 + - - -
285A GLN* 4.0 6.8 - - - +
286A THR* 3.8 15.6 - - - +
403A MG 3.9 7.7 - - - -
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Residues in contact with PHE 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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201A LEU* 4.3 26.7 - - + +
202A GLN* 3.2 42.2 - - + -
255A LEU 2.8 19.3 + - - +
256A ALA* 3.2 8.5 + - - +
258A ARG* 1.3 76.9 - - - +
260A LYS* 1.3 62.8 + - - +
261A GLU 3.4 0.5 + - - -
262A SER 3.4 14.5 + - - +
263A PRO* 4.4 12.0 - - + +
264A PHE* 3.5 46.0 - + + -
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Residues in contact with LYS 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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256A ALA 3.3 11.4 + - - +
257A LYS* 3.9 10.3 - - - +
258A ARG 3.2 0.8 - - - -
259A PHE* 1.3 79.2 - - - +
261A GLU* 1.3 61.6 + - + +
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Residues in contact with GLU 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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257A LYS* 3.3 35.9 + - - +
258A ARG* 3.1 25.2 + - - +
259A PHE 4.2 0.4 - - - -
260A LYS* 1.3 83.6 - - + +
262A SER* 1.3 61.5 + - - +
263A PRO* 4.6 1.7 - - - +
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Residues in contact with SER 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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258A ARG* 2.9 33.3 + - - +
259A PHE* 3.4 13.2 - - - -
261A GLU* 1.3 78.5 - - - +
263A PRO* 1.3 71.8 - - - +
264A PHE* 3.6 6.1 - - - -
285A GLN* 3.2 27.4 + - - +
403A MG 2.1 27.3 - - - -
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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