Contacts of the helix formed by residues 251 - 255 (chain B) in PDB entry 3FVS
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 ALA 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASN 3.0 14.1 - - - +
62A GLN* 3.9 1.1 - - - +
42B PRO* 4.1 9.4 - - + -
245B ALA 5.1 0.2 - - - +
246B GLY* 2.9 18.0 + - - -
249B PHE* 3.3 10.5 - - + +
250B SER* 1.3 77.0 - - - +
252B THR* 1.3 63.8 + - - +
254B TRP* 3.0 55.5 + - + +
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Residues in contact with THR 252 (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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62A GLN* 2.7 27.3 + - - +
63A TYR* 3.0 53.3 + - + -
36B GLY 4.4 0.9 - - - +
37B PHE* 3.4 20.6 - - + +
38B PRO* 4.5 0.4 - - + -
246B GLY* 3.8 18.9 - - - +
247B LLP 4.0 30.0 + - + -
251B ALA* 1.3 75.8 - - - +
253B GLY* 1.3 58.5 + - - +
254B TRP 3.1 1.5 + - - -
255B LYS* 3.4 12.9 + - - +
338B TYR* 4.4 5.8 - - - +
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Residues in contact with GLY 253 (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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61A ASN 2.7 21.9 + - - -
62A GLN 3.3 24.1 - - - -
63A TYR* 3.7 2.9 - - - -
281A PRO* 3.2 6.4 - - - +
282A THR* 2.9 31.9 + - - -
283A GLN* 4.7 2.8 + - - +
252B THR* 1.3 69.7 - - - +
254B TRP* 1.3 66.4 + - - +
255B LYS* 3.3 3.6 - - - -
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Residues in contact with TRP 254 (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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61A ASN* 3.0 27.6 + - - -
281A PRO* 3.8 12.2 - - - +
283A GLN* 3.4 18.9 + - - -
46B ALA* 3.2 45.8 - - + -
47B VAL* 4.4 3.1 - - + -
50B PHE* 3.6 25.8 - + + -
245B ALA* 4.9 5.6 - - + -
246B GLY* 5.2 3.6 - - - +
249B PHE* 5.1 6.3 - + + -
251B ALA* 3.0 34.8 + - + +
253B GLY* 1.3 81.4 - - - +
255B LYS* 1.3 69.0 + - - +
256B VAL* 3.3 17.7 + - + +
284B SER* 4.4 10.4 + - - -
287B ALA* 3.9 25.1 - - + -
288B VAL* 3.7 27.6 - - + -
291B SER* 4.4 5.4 - - - -
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Residues in contact with LYS 255 (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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63A TYR* 3.7 14.1 - - + -
277A VAL 2.9 20.0 + - - -
279A HIS* 3.0 57.4 - - + +
280A CYS 4.2 0.9 - - - +
281A PRO* 4.0 23.6 - - + +
97B THR 4.1 0.2 - - - +
98B VAL* 3.6 24.6 - - + +
99B GLY* 3.2 16.7 + - - -
101B TYR* 3.5 5.7 - - - +
246B GLY* 5.4 2.4 - - - +
247B LLP 2.8 30.8 + - - +
251B ALA 4.4 0.4 + - - -
252B THR 3.4 11.8 + - - +
253B GLY* 4.2 5.2 - - - +
254B TRP* 1.3 81.4 - - - +
256B VAL* 1.3 59.1 - - - +
281B PRO* 5.8 3.3 - - - +
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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