Contacts of the helix formed by residues 297 - 302 (chain B) in PDB entry 7CE1
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 PHE 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.7 25.1 - - + -
91A MET* 3.4 22.4 - - + -
270A ILE* 4.9 1.0 - - - +
91B MET* 3.4 45.8 - - + -
93B PHE* 4.0 13.9 - + + -
266B GLY* 4.2 11.7 - - - -
270B ILE* 4.4 2.7 - - + -
293B GLN* 3.0 12.3 - - + +
294B SER 5.3 0.7 - - - -
295B ALA 2.7 19.4 + - - +
296B GLU* 1.3 74.2 - - - +
298B LEU* 1.3 91.9 + - + +
299B ASN* 3.5 2.7 - - - -
300B TRP* 3.7 13.0 + - - +
301B ILE* 3.3 43.6 + - + +
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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
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266B GLY* 4.5 6.3 - - - +
269B THR* 4.7 10.5 - - + -
270B ILE* 3.6 33.0 - - + -
291B SER* 3.9 26.9 - - - +
292B LYS 4.4 3.6 - - - +
293B GLN* 2.6 33.8 - - + +
297B PHE* 1.3 92.8 - - + +
299B ASN* 1.3 53.3 + - - +
300B TRP 3.3 2.0 - - - -
301B ILE* 3.1 7.2 + - + +
302B GLN* 2.5 37.7 + - - +
305B ILE* 4.9 10.1 - - + -
307B THR* 3.8 19.1 - - + -
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Residues in contact with ASN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ALA* 5.5 1.4 - - - +
293B GLN* 4.2 2.9 + - - -
296B GLU* 3.7 33.7 + - - +
297B PHE 4.3 0.2 - - - -
298B LEU* 1.3 74.3 + - - +
300B TRP* 1.3 68.8 + - - +
301B ILE 3.1 0.7 - - - -
302B GLN 3.3 13.5 - - - +
303B PRO* 3.6 29.8 - - + +
305B ILE 5.0 2.0 - - - +
307B THR* 4.5 15.5 + - + +
344B SER* 4.2 5.5 + - - -
345B SER 3.9 19.4 + - - -
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Residues in contact with TRP 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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90A LEU* 5.5 2.0 - - + -
241A LEU* 3.6 45.7 + - + -
242A ASP* 4.0 17.5 - - + -
245A ARG* 4.5 6.8 - - + +
270A ILE* 3.4 25.7 - - + +
271A ALA* 3.7 26.7 - - + +
273A VAL* 6.1 0.2 - - - +
274A ALA* 3.7 31.2 - - + +
296B GLU* 3.3 49.6 - - + -
297B PHE* 3.7 9.3 + - - +
298B LEU 3.3 0.2 - - - -
299B ASN* 1.3 87.7 + - - +
301B ILE* 1.3 59.5 + - - +
303B PRO* 5.6 1.1 - - - +
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Residues in contact with ILE 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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91A MET* 4.7 0.7 - - + -
270A ILE* 4.0 19.5 - - + -
301A ILE* 3.4 57.2 - - + +
91B MET* 5.3 1.1 - - + -
270B ILE* 3.9 16.4 - - + -
273B VAL* 6.3 2.0 - - + -
297B PHE* 3.3 49.4 - - + +
298B LEU* 3.1 8.4 + - + +
300B TRP* 1.3 82.6 - - - +
302B GLN* 1.3 77.5 + - + +
303B PRO* 4.3 3.1 - - - +
305B ILE* 6.3 0.2 - - + -
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Residues in contact with GLN 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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301A ILE* 4.6 5.2 - - - +
273B VAL* 5.4 8.8 - - - +
277B GLU* 3.6 22.4 + - - +
283B ILE* 4.0 21.0 - - + +
298B LEU 2.5 19.3 + - - +
299B ASN* 3.3 7.4 - - - +
301B ILE* 1.3 101.2 - - + +
303B PRO* 1.3 71.0 - - - +
304B GLN* 3.3 20.4 + - - +
305B ILE* 3.4 46.8 + - + +
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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