Contacts of the strand formed by residues 450 - 456 (chain B) in PDB entry 3GHG
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 MET 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B GLN* 3.9 5.2 - - - +
255B ARG* 2.6 45.5 + - + +
312B ILE* 3.8 27.4 - - - -
313B GLU 3.5 8.9 + - - -
314B MET* 3.9 20.2 - - - +
412B PRO* 3.6 37.9 - - + -
435B VAL* 3.2 34.5 - - + -
436B VAL 4.3 12.6 - - - +
437B TRP* 3.9 19.7 - - + +
447B MET* 4.5 2.9 - - + -
449B LYS* 1.3 78.1 - - - +
451B SER* 1.3 60.9 + - - +
452B MET* 5.9 0.2 - - + -
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Residues in contact with SER 451 (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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251B VAL* 5.8 0.9 - - - -
253B GLN* 3.0 13.9 - - - +
254B ASN* 3.6 17.9 - - - -
312B ILE* 3.2 11.1 - - - +
313B GLU* 2.8 48.8 + - - +
449B LYS* 6.4 0.2 - - - -
450B MET* 1.3 80.7 + - - +
452B MET* 1.3 60.5 + - - +
453B LYS* 4.4 15.5 + - - -
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Residues in contact with MET 452 (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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251B VAL* 3.6 3.8 - - - +
252B ILE* 2.9 29.6 + - + -
253B GLN* 2.8 43.1 + - + +
293B TRP* 4.4 6.3 - - - -
310B LEU* 3.8 22.2 - - + -
311B LEU 3.6 7.0 - - - +
312B ILE* 3.8 30.7 - - + -
329B PHE* 5.6 4.3 - - + -
353B LEU* 5.6 2.0 - - + -
402B TRP* 4.0 35.0 - - + -
403B TRP* 5.5 3.8 - - + -
412B PRO* 5.0 5.4 - - + -
451B SER* 1.3 79.8 - - - +
453B LYS* 1.3 68.2 + - - +
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Residues in contact with LYS 453 (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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241B ASP* 3.0 29.0 + - - +
244B THR* 4.8 1.0 - - - +
249B TRP* 3.6 30.6 - - + -
250B THR 3.0 22.0 - - - +
251B VAL* 4.0 16.1 - - - +
252B ILE* 4.0 4.6 - - - +
310B LEU* 3.4 5.0 - - - +
311B LEU* 2.9 47.1 + - + +
313B GLU* 3.9 22.5 + - + +
451B SER* 4.4 20.2 + - - -
452B MET* 1.3 82.9 - - - +
454B ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 454 (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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248B GLY 3.9 0.2 - - - +
249B TRP* 3.5 4.4 - - - -
250B THR* 2.9 38.2 + - - +
252B ILE* 2.9 42.0 - - + -
299B ILE* 4.8 1.1 - - + +
302B LEU* 4.2 31.4 - - + -
303B THR* 4.4 11.4 - - + -
308B THR* 3.8 9.4 - - + -
309B GLU 3.2 11.2 - - - +
310B LEU* 3.7 3.8 - - + -
329B PHE* 3.4 27.4 - - + -
453B LYS* 1.3 77.7 - - - +
455B ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 455 (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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212B GLU* 4.4 13.7 + - + +
245B GLU* 2.9 22.2 + - - +
246B ASN* 4.1 12.5 + - - +
247B GLY 2.6 31.5 + - - -
248B GLY* 3.5 23.3 - - - +
249B TRP* 3.5 29.7 - - + +
250B THR* 5.5 1.1 - - - -
308B THR* 3.5 4.9 - - - -
309B GLU* 2.8 53.9 + - + +
325B HIS* 5.8 1.6 + - - -
454B ILE* 1.3 81.2 - - - +
456B PRO* 1.3 83.8 + - + +
458B PHE* 6.3 0.2 - - + -
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Residues in contact with PRO 456 (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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210B GLU* 3.8 27.8 - - + +
212B GLU* 4.1 17.9 - - + -
248B GLY 5.0 0.2 - - - +
250B THR* 6.1 0.2 - - - +
305B MET* 4.9 11.9 - - + -
306B GLY 6.1 0.4 - - - -
307B PRO* 3.4 12.8 - - + +
308B THR* 4.3 2.9 - - - +
309B GLU* 4.2 6.3 - - - +
455B ARG* 1.3 108.3 + - + +
457B PHE* 1.3 64.3 + - - +
458B PHE* 4.2 21.0 - - + -
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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