Contacts of the helix formed by residues 320 - 326 (chain B) in PDB entry 2GFP
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 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B MET* 3.4 27.1 - - + +
316B LEU 5.0 0.4 - - - -
317B PHE 2.8 13.9 + - - +
318B PRO* 2.7 3.9 + - + +
319B LEU* 1.3 77.3 - - - +
321B THR* 1.3 60.7 + - - +
323B GLY* 4.3 0.4 - - - -
324B ALA* 2.8 31.9 + - - +
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Residues in contact with THR 321 (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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192B PRO* 3.5 32.8 - - + +
193B ARG 4.7 0.9 - - - +
194B THR* 4.0 20.6 - - - +
318B PRO 3.4 6.8 + - - -
320B ALA* 1.3 81.4 - - - +
322B SER* 1.3 62.8 + - - +
324B ALA* 3.4 4.4 + - - +
325B MET* 3.2 21.5 + - - +
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Residues in contact with SER 322 (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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194B THR* 5.4 7.7 - - - -
199B SER* 5.7 2.5 - - - -
318B PRO 3.7 6.9 + - - -
319B LEU* 3.4 31.6 - - - +
320B ALA 3.3 1.6 - - - +
321B THR* 1.3 82.2 - - - +
323B GLY* 1.3 56.0 + - - +
325B MET* 3.2 27.7 - - - +
326B GLU* 2.9 28.9 + - - +
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Residues in contact with GLY 323 (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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314B GLY 4.3 6.1 - - - -
315B MET* 5.1 3.8 - - - -
319B LEU 2.7 28.5 + - - -
320B ALA* 3.8 1.1 - - - -
322B SER* 1.3 74.8 - - - +
324B ALA* 1.3 66.9 + - - +
325B MET 2.9 0.9 - - - -
326B GLU* 3.0 14.8 + - - -
327B PRO* 2.7 31.8 - - - +
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Residues in contact with ALA 324 (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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61B LEU* 4.2 13.2 - - + -
192B PRO* 4.5 11.9 - - + -
315B MET* 5.1 6.1 - - + +
320B ALA 2.8 21.2 + - - +
321B THR* 3.6 6.1 - - - +
323B GLY* 1.3 73.2 - - - +
325B MET* 1.3 55.0 + - - +
328B PHE* 3.1 34.9 + - + +
329B PRO* 2.7 26.7 - - - +
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Residues in contact with MET 325 (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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192B PRO* 5.8 0.4 - - - +
193B ARG* 6.5 0.7 - - - -
194B THR* 4.9 16.2 - - - +
195B ARG* 4.7 23.6 - - - +
196B LEU* 4.7 10.1 - - + -
199B SER* 5.2 4.5 - - - +
321B THR 3.2 11.9 + - - +
322B SER* 3.2 29.8 - - - +
323B GLY 2.9 0.4 - - - -
324B ALA* 1.3 79.1 - - - +
326B GLU* 1.3 76.0 + - - +
329B PRO* 3.0 22.0 - - + +
330B PHE* 2.9 63.8 + - + -
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Residues in contact with GLU 326 (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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206B ASN* 5.8 8.6 - - - +
209B PHE* 6.1 0.3 - - - +
210B ASN* 6.4 2.0 - - - -
310B PHE* 3.6 27.8 - - + -
314B GLY* 4.9 9.0 - - - -
319B LEU* 3.9 31.2 - - - +
322B SER 2.9 18.1 + - - +
323B GLY* 3.0 7.3 + - - +
325B MET* 1.3 74.9 - - + +
327B PRO* 1.4 75.8 - - + +
330B PHE* 2.8 43.8 - - + +
331B LEU* 3.4 4.1 + - - +
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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