Contacts of the helix formed by residues 295 - 299 (chain A) in PDB entry 3URF
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLY 4.5 6.0 + - - -
180A HIS 4.5 1.2 + - - -
222A PHE* 3.7 5.2 - - - -
233A THR* 5.6 1.2 - - - +
236A LEU* 4.0 15.2 - - - +
237A GLN 2.9 33.9 + - - +
238A LEU* 3.9 10.6 - - + +
294A SER* 1.3 76.1 - - - +
296A PRO* 1.3 76.1 - - - +
297A SER* 3.2 5.1 + - - -
298A LEU* 3.1 38.4 + - + +
94Z ILE* 4.8 5.5 - - - +
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Residues in contact with PRO 296 (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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175A ILE* 4.9 6.2 - - - +
176A PRO* 3.2 34.3 - - + +
178A GLY 3.9 16.2 - - - +
182A VAL* 3.6 32.3 - - + -
184A LEU* 4.7 0.9 - - + -
293A VAL* 4.1 14.1 - - + +
294A SER 3.4 0.6 - - - -
295A ASN* 1.3 86.7 - - - +
297A SER* 1.3 63.1 - - - +
298A LEU 2.9 11.2 + - - -
299A LEU* 2.9 39.0 + - + +
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Residues in contact with SER 297 (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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175A ILE* 5.4 10.8 - - - -
176A PRO 4.1 4.6 + - - -
177A SER* 4.7 18.4 + - - -
178A GLY 5.3 0.7 + - - -
223A ARG 5.2 0.2 - - - +
224A HIS* 5.6 1.2 - - - -
295A ASN* 4.2 4.0 + - - -
296A PRO* 1.3 81.6 - - - +
298A LEU* 1.3 64.9 + - - +
299A LEU 3.3 3.6 - - - +
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Residues in contact with LEU 298 (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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222A PHE* 3.2 11.9 - - + -
223A ARG* 2.6 46.6 + - - +
224A HIS* 3.5 37.0 - - + -
231A LEU* 5.4 3.1 - - + -
236A LEU* 3.9 29.6 - - + -
238A LEU* 4.3 4.5 - - + -
264A TRP* 4.1 5.6 - - + -
295A ASN* 3.4 34.3 - - + +
296A PRO 2.9 1.4 + - - -
297A SER* 1.3 85.0 - - - +
299A LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 299 (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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170A ILE* 5.0 4.5 - - + -
175A ILE* 4.8 15.3 - - + -
184A LEU* 3.8 32.8 - - + -
220A ILE* 3.4 26.9 - - + -
221A CYS 3.3 14.1 - - - +
222A PHE* 4.0 12.1 - - + -
223A ARG* 4.3 3.2 - - - +
293A VAL* 4.2 4.0 - - + -
296A PRO* 2.9 35.0 + - + +
297A SER 3.3 2.7 - - - +
298A LEU* 1.3 80.4 - - - +
300A ASP* 1.3 67.2 + - - +
301A PRO* 3.6 8.2 - - + +
306A THR* 4.4 11.2 - - + +
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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