Contacts of the helix formed by residues 334 - 342 (chain A) in PDB entry 2O2C
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 GLY 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A MET* 3.9 7.2 - - - -
329A MET 3.3 23.0 + - - -
331A SER 2.9 10.7 + - - -
333A ILE* 1.3 77.6 - - - +
335A LEU* 1.3 62.1 + - - +
336A PRO 3.4 1.3 - - - -
337A ILE* 3.0 28.6 + - - +
338A MET* 3.0 11.1 + - - +
346A PHE* 3.5 7.3 - - - -
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Residues in contact with LEU 335 (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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177A MET* 3.7 44.8 - - + +
180A PHE* 3.9 25.6 - - + -
181A SER* 4.6 2.0 - - - -
255A ILE* 4.3 10.5 - - + -
297A VAL* 4.4 3.6 - - + -
299A LEU* 3.7 21.3 - - + -
317A PHE* 3.9 22.2 - - + -
332A ALA 2.9 17.8 + - - +
333A ILE 3.1 1.8 - - - -
334A GLY* 1.3 75.6 - - - +
336A PRO* 1.4 62.3 - - + +
338A MET* 3.1 4.6 + - + +
339A ILE* 2.9 43.6 + - + +
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Residues in contact with PRO 336 (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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200A VAL* 5.0 0.4 - - + -
202A ASN* 3.5 30.3 - - + +
212A PRO* 3.9 20.2 - - + -
216A THR* 4.0 4.8 - - + +
229A LEU* 4.0 23.1 - - + +
231A PHE* 4.8 1.1 - - + -
255A ILE* 4.2 19.1 - - + -
299A LEU* 4.1 5.4 - - + -
333A ILE 3.3 14.8 - - - +
335A LEU* 1.4 91.9 - - + +
337A ILE* 1.3 60.8 + - - +
339A ILE* 3.9 5.8 - - + +
340A SER* 3.1 23.6 + - - -
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Residues in contact with ILE 337 (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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211A GLY 4.2 2.0 - - - +
212A PRO* 4.0 26.2 - - + -
215A ALA* 3.7 35.4 - - + +
216A THR* 3.9 12.6 - - + -
219A LEU* 5.0 0.4 - - + -
329A MET* 3.9 23.1 - - + +
334A GLY* 3.0 25.7 + - - +
336A PRO* 1.3 78.0 - - - +
338A MET* 1.3 58.2 + - - +
340A SER* 3.2 3.1 + - - -
341A ILE* 2.9 55.0 + - + +
346A PHE* 4.0 10.8 - - + -
349A LEU* 4.2 4.9 - - + -
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Residues in contact with MET 338 (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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174A LEU* 4.2 7.4 - - + +
177A MET* 3.5 40.8 - - + +
178A ARG* 3.7 5.4 - - - -
181A SER* 3.5 24.0 - - - +
185A ARG* 4.1 2.8 - - - -
334A GLY 3.0 11.1 + - - +
335A LEU* 3.1 11.2 + - + +
337A ILE* 1.3 75.1 - - - +
339A ILE* 1.3 59.2 - - - +
341A ILE* 4.5 0.2 - - - -
342A GLY* 2.7 34.6 + - - +
343A TYR* 3.7 37.9 - - + +
346A PHE* 3.6 37.0 - - + -
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Residues in contact with ILE 339 (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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180A PHE* 4.1 8.7 - - + -
181A SER* 4.0 23.6 - - - -
184A VAL* 3.9 24.0 - - + -
185A ARG* 3.0 28.3 + - + +
200A VAL* 3.9 19.1 - - + -
227A LEU* 3.6 12.9 - - + +
229A LEU* 5.3 1.3 - - + -
253A LEU* 4.0 18.2 - - + -
255A ILE* 3.8 28.7 - - + -
335A LEU* 2.9 28.0 + - + +
336A PRO* 3.9 6.1 - - + +
337A ILE 3.3 0.4 - - - -
338A MET* 1.3 74.8 - - - +
340A SER* 1.3 59.2 + - - +
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Residues in contact with SER 340 (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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185A ARG* 2.9 8.1 + - - -
216A THR* 4.1 18.9 + - - +
223A SER* 3.3 19.8 - - - -
224A GLN* 2.9 31.2 + - - +
227A LEU* 5.2 3.2 + - - -
229A LEU* 4.0 22.7 - - - +
336A PRO 3.1 18.0 + - - -
337A ILE 3.2 3.8 + - - -
339A ILE* 1.3 78.3 - - - +
341A ILE* 1.3 61.0 + - - +
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Residues in contact with ILE 341 (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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185A ARG* 3.7 7.6 + - - -
215A ALA 5.4 0.9 - - - +
216A THR* 5.6 2.9 - - - -
219A LEU* 3.6 56.3 - - + +
222A PHE* 3.5 18.0 - - + +
223A SER* 4.3 1.8 - - - +
337A ILE* 2.9 39.9 + - + +
338A MET* 4.5 0.9 - - - -
340A SER* 1.3 81.4 - - - +
342A GLY* 1.3 63.5 + - - +
345A ASN* 3.0 57.6 + - + +
346A PHE* 4.0 5.6 - - + +
349A LEU* 4.9 1.8 - - + -
536A PRO* 4.7 0.7 - - + -
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Residues in contact with GLY 342 (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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182A GLU* 5.1 0.9 - - - -
185A ARG* 3.3 26.1 - - - +
338A MET* 2.7 25.8 + - - -
341A ILE* 1.3 75.5 - - - +
343A TYR* 1.3 60.4 + - - -
344A GLU 3.4 2.2 - - - -
345A ASN 3.4 1.5 + - - -
346A PHE* 3.0 28.1 + - - +
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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