Contacts of the helix formed by residues 250 - 255 (chain A) in PDB entry 3FZ7
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 LEU 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A TYR* 3.6 10.3 - - - +
246A SER 3.5 18.6 - - - +
247A GLY* 2.9 5.6 + - - +
248A GLY 3.5 0.4 - - - -
249A PHE* 1.3 79.4 - - - +
251A ALA* 1.3 67.7 + - - +
252A PRO* 3.3 1.8 - - - -
253A PHE* 3.0 17.8 + - - +
254A VAL* 3.1 16.2 + - - +
277A PHE* 3.7 31.6 - - + -
343A GLN* 3.7 28.9 - - + +
347A TYR* 3.6 12.1 - - + +
375A ILE* 3.5 37.2 - - + -
376A PRO* 3.5 16.6 - - + -
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Residues in contact with ALA 251 (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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209A PHE* 3.6 36.1 - - + -
217A TYR* 3.8 10.8 - - + +
247A GLY 3.2 2.0 + - - -
250A LEU* 1.3 77.5 - - - +
252A PRO* 1.3 69.9 - - + +
254A VAL* 4.4 3.6 - - - -
255A ALA* 2.9 42.4 + - - +
258A ILE* 4.7 4.7 - - + -
260A TRP* 3.8 9.6 - - + +
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Residues in contact with PRO 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.7 37.7 - - + +
108A TRP* 4.2 2.5 - - + -
109A HIS* 6.3 1.8 - - + -
247A GLY 3.7 2.7 - - - +
248A GLY 3.3 26.9 - - - +
249A PHE 4.1 1.8 - - - -
250A LEU 3.3 8.1 - - - +
251A ALA* 1.3 93.8 - - + +
253A PHE* 1.4 59.2 + - + +
256A PRO* 3.7 21.6 - - + +
260A TRP* 3.7 22.0 - - + +
261A ASP* 5.9 0.7 - - - +
336A ARG* 4.2 13.8 + - - +
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Residues in contact with PHE 253 (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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107A LEU* 3.7 32.5 - - + -
249A PHE* 3.2 41.7 - + + -
250A LEU 3.0 4.1 + - - +
252A PRO* 1.4 82.4 - - + +
254A VAL* 1.3 65.4 + - + +
255A ALA 3.5 1.0 + - - -
256A PRO* 4.2 7.8 - - - +
336A ARG* 4.0 20.6 - - + -
339A TYR* 3.5 46.9 - + + +
340A THR* 3.5 35.7 + - - +
343A GLN* 4.3 3.4 - - + -
32F PHE* 3.7 23.8 - + - -
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Residues in contact with VAL 254 (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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250A LEU 3.1 15.6 + - - +
251A ALA* 4.4 1.1 - - - -
253A PHE* 1.3 79.8 - - + +
255A ALA* 1.3 66.4 + - + +
256A PRO* 3.8 3.3 - - - +
340A THR* 4.1 7.9 - - + +
343A GLN* 4.0 25.6 - - + -
344A ASN* 3.3 35.0 - - - +
347A TYR* 3.8 15.9 - - + +
371A PRO* 3.8 29.6 - - + +
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Residues in contact with ALA 255 (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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251A ALA* 2.9 18.1 + - - +
254A VAL* 1.3 84.7 - - + +
256A PRO* 1.3 66.6 - - - +
257A ASP* 3.0 17.1 + - - +
258A ILE* 3.1 42.5 + - + +
260A TRP* 5.5 0.2 + - - -
371A PRO* 4.1 14.6 - - + +
372A ASP* 5.2 2.7 - - + -
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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