Contacts of the helix formed by residues 294 - 303 (chain B) in PDB entry 2IVF
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 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE* 3.4 36.3 - - + -
292B ARG 3.2 9.6 - - - +
293B ILE* 1.3 89.7 - - + +
295B LEU* 1.3 67.7 + - - +
296B ASP* 3.5 16.8 - - - +
297B VAL* 3.2 20.1 + - + +
298B LEU 3.4 7.6 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ILE 3.3 5.6 + - - +
294B PRO* 1.3 74.2 - - - +
296B ASP* 1.3 58.5 + - - +
298B LEU* 3.1 6.2 + - - +
299B GLU* 2.8 52.9 + - + +
306B VAL* 3.4 33.4 - - + -
307B LYS* 3.8 44.2 - - + +
310B LEU* 4.4 9.4 - - + -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PRO* 3.5 17.7 - - - +
295B LEU* 1.3 75.8 + - - +
297B VAL* 1.3 66.5 + - - +
299B GLU* 3.6 17.9 - - - +
300B GLY* 2.9 24.9 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.6 34.0 + - + +
60B PRO* 5.0 2.2 - - + -
143B PHE* 4.2 21.1 - - + -
145B PHE* 5.6 0.7 - - + -
293B ILE* 5.1 0.4 - - + -
294B PRO* 3.4 32.5 - - + +
295B LEU 3.1 0.2 - - - -
296B ASP* 1.3 79.9 + - - +
298B LEU* 1.3 70.3 + - + +
300B GLY* 3.1 11.8 + - - -
301B LEU* 3.5 13.2 + - - +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.8 33.9 - - + -
274B PRO* 4.6 2.0 - - + -
275B PRO* 3.6 38.6 - - + +
291B THR* 6.3 0.4 - - + -
293B ILE* 3.6 27.6 - - + +
294B PRO 3.4 2.2 + - - +
295B LEU* 3.1 8.7 + - - +
297B VAL* 1.3 79.5 - - + +
299B GLU* 1.3 57.2 + - - +
301B LEU* 3.1 3.6 + - + +
302B PHE* 2.8 41.7 + - + +
306B VAL* 3.7 28.0 - - + -
310B LEU* 4.2 10.1 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 2.8 48.4 + - + +
296B ASP* 3.6 18.4 - - - +
298B LEU* 1.3 74.9 - - - +
300B GLY* 1.3 63.7 + - - +
303B GLY* 2.9 44.1 + - - +
304B PRO* 4.5 14.5 - - + +
306B VAL* 4.3 2.7 - - + -
307B LYS* 5.1 2.8 - - - +
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B HIS* 3.4 21.9 + - - -
263B GLU* 3.8 9.2 - - - +
296B ASP 2.9 15.0 + - - -
297B VAL* 3.1 6.6 + - - -
299B GLU* 1.3 78.0 - - - +
301B LEU* 1.3 61.7 + - - +
303B GLY 5.1 0.2 + - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.8 47.1 - - + +
68B TYR* 5.3 0.2 - - - +
69B GLU* 3.5 25.4 - - - +
145B PHE* 4.1 7.4 - - + -
147B LEU* 4.4 9.2 - - + -
259B PRO 3.4 2.1 - - - +
260B LEU* 3.5 12.8 - - + -
261B HIS* 2.8 41.9 + - + +
263B GLU* 5.7 0.2 - - - -
297B VAL 4.0 9.9 - - - +
298B LEU* 3.1 8.4 + - + +
300B GLY* 1.3 80.1 - - - +
302B PHE* 1.3 88.9 + - + +
303B GLY 3.7 0.4 - - - -
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.5 31.6 - - + -
145B PHE* 4.7 1.6 - + - -
147B LEU* 4.3 7.0 - - + -
258B LEU* 3.6 40.4 - - + +
259B PRO* 3.5 21.2 - - - +
260B LEU* 4.0 14.1 - - + -
262B ALA 6.3 0.2 - - - -
272B TYR* 3.6 27.1 - + + -
274B PRO* 4.3 18.2 - - + -
298B LEU* 2.8 33.6 + - + +
301B LEU* 1.3 100.7 - - + +
303B GLY* 1.3 62.6 + - - +
305B GLU* 4.8 1.4 + - - +
306B VAL* 3.7 10.3 - - + -
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 5.9 2.8 + - - -
299B GLU* 2.9 26.8 + - - +
300B GLY 5.1 0.2 + - - -
301B LEU 3.7 0.8 - - - -
302B PHE* 1.3 77.3 - - - +
304B PRO* 1.3 68.7 - - - +
305B GLU 3.2 6.7 + - - -
306B VAL* 3.2 23.4 + - - +
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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