Contacts of the helix formed by residues 258 - 263 (chain A) in PDB entry 4L7H
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 PRO 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A LYS 4.8 0.9 - - - +
257A PHE* 1.3 93.8 - - + +
259A ASP* 1.3 65.7 + - - +
261A PHE* 3.1 22.2 + - + +
262A TRP* 3.6 5.9 - - - -
266A GLN* 3.2 34.3 - - - +
267A LEU 5.8 0.9 - - - +
268A VAL* 4.6 9.2 - - + -
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Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LYS* 4.9 10.4 + - - -
257A PHE 3.8 1.9 + - - +
258A PRO* 1.3 71.7 - - - +
260A GLY* 1.3 58.8 + - - +
262A TRP* 3.0 13.2 + - - +
263A LEU* 2.9 42.9 + - + +
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Residues in contact with GLY 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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258A PRO 3.1 1.6 - - - -
259A ASP* 1.3 78.7 - - - +
261A PHE* 1.3 55.1 + - - +
263A LEU* 3.4 12.0 + - - +
264A GLY 3.2 2.1 + - - -
265A GLU* 2.7 37.9 + - - +
266A GLN* 2.8 36.1 + - - +
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Residues in contact with PHE 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 PHE* 3.7 26.5 - + + -
258A PRO* 3.1 14.3 + - + +
259A ASP 3.1 1.0 + - - -
260A GLY* 1.3 72.6 - - - +
262A TRP* 1.3 91.9 + + - +
263A LEU 3.0 4.0 - - - -
264A GLY* 2.7 21.5 + - - -
266A GLN* 3.5 24.1 - - + +
268A VAL* 3.5 37.2 - - + -
270A TRP* 5.9 1.1 - + - -
280A PHE* 4.8 9.2 - + - -
306A LEU* 3.8 26.2 - - + -
320A TYR* 4.3 8.3 - - + -
322A PHE* 3.2 42.4 - + + +
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Residues in contact with TRP 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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241A PHE* 3.9 14.9 - - - -
245A VAL* 4.5 9.9 - - + +
248A ILE* 3.5 36.3 - - + -
249A LYS* 3.6 50.7 - - + +
252A SER* 3.9 14.4 - - - -
257A PHE* 3.7 38.4 + + - +
258A PRO 3.6 20.4 - - - -
259A ASP* 3.0 11.3 + - - +
261A PHE* 1.3 98.2 - + - +
263A LEU* 1.3 62.5 + - + +
264A GLY 3.1 1.8 + - - -
280A PHE* 4.5 4.7 - + - -
322A PHE* 3.5 40.3 - + - -
324A ILE 4.6 0.2 - - - +
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Residues in contact with LEU 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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241A PHE* 5.6 9.2 - - + -
259A ASP* 2.9 34.0 + - + +
260A GLY* 3.7 11.2 - - - +
261A PHE 3.0 0.2 - - - -
262A TRP* 1.3 80.6 - - + +
264A GLY* 1.3 61.6 + - - +
265A GLU* 3.2 10.2 + - + +
324A ILE 5.6 2.0 - - - -
325A SER* 5.6 4.9 - - - -
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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