Contacts of the strand formed by residues 325 - 330 (chain I) in PDB entry 5GJQ
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 VAL 325 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I LYS 5.4 1.2 - - - +
271I PHE* 3.9 20.9 - - + -
274I ALA* 4.2 13.7 - - + -
275I GLU* 4.3 10.8 - - + +
280I SER* 3.9 4.5 - - - +
282I VAL* 3.4 33.9 - - + -
322I ARG* 3.4 44.9 - - + +
323I GLY 3.2 8.1 + - - +
324I ASP* 1.3 79.4 - - - +
326I LYS* 1.3 65.6 - - - +
327I VAL* 4.2 10.4 - - + +
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Residues in contact with LYS 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I SER 4.8 1.8 + - - -
201I VAL* 4.5 32.9 - - + +
204I PRO* 5.0 4.9 - - - +
205I LEU* 6.3 3.4 - - + -
218I PRO* 2.6 47.5 - - - +
219I PRO 4.7 1.8 + - - -
220I LYS* 4.2 14.3 + - - +
280I SER 3.3 13.8 + - - +
281I ILE* 3.7 16.0 - - + -
282I VAL* 2.9 32.1 + - - +
323I GLY 5.6 1.3 - - - -
324I ASP* 3.5 27.1 + - - +
325I VAL* 1.3 76.2 - - - +
327I VAL* 1.3 60.8 + - - +
328I ILE* 6.1 1.1 - - + -
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Residues in contact with VAL 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I VAL* 5.8 1.8 - - - +
220I LYS 4.5 7.6 + - - +
221I GLY* 3.9 15.3 - - - +
222I VAL* 2.8 34.7 + - - +
282I VAL* 3.3 7.9 - - + +
284I ILE* 5.0 5.8 - - + -
316I LEU* 3.3 50.0 - - + +
325I VAL* 4.2 16.4 - - + +
326I LYS* 1.3 78.9 - - - +
328I ILE* 1.3 68.6 + - - +
329I MET* 4.1 16.8 - - + -
346I ARG 5.1 1.1 - - - +
347I ILE* 4.8 1.8 - - + -
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Residues in contact with ILE 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ILE* 4.8 20.6 - - + -
201I VAL* 5.2 10.1 - - + -
222I VAL* 3.6 5.2 - - + +
224I LEU* 4.7 18.2 - - + -
235I LEU* 5.6 1.8 - - + -
236I ALA* 4.7 8.1 - - + +
239I VAL* 5.2 9.4 - - + -
247I PHE* 4.7 6.1 - - + -
281I ILE* 3.8 28.7 - - + -
282I VAL 2.9 9.2 + - - +
283I PHE* 2.5 51.8 - - + -
284I ILE 2.4 34.4 + - - -
326I LYS* 6.1 0.7 - - + -
327I VAL* 1.3 81.8 - - - +
329I MET* 1.3 59.3 + - - +
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Residues in contact with MET 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222I VAL 3.2 7.1 + - - +
223I ILE* 3.7 10.0 - - + +
224I LEU* 2.7 36.0 + - - +
284I ILE* 3.0 18.6 - - - +
287I ILE* 3.2 40.2 - - + -
312I LEU* 4.5 1.3 - - - -
316I LEU* 4.1 15.7 - - + -
327I VAL* 4.1 8.1 - - + -
328I ILE* 1.3 77.6 - - - +
330I ALA* 1.3 60.5 + - - +
331I THR 3.9 0.9 - - - -
337I LEU* 5.3 1.3 - - + -
341I LEU* 4.3 26.9 - - + -
342I ILE* 5.3 1.1 - - + -
347I ILE* 3.0 38.4 - - + -
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Residues in contact with ALA 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I LEU* 3.5 6.1 - - + -
232I LYS* 4.5 20.4 - - + -
283I PHE* 3.6 15.3 - - + -
284I ILE 2.7 8.1 + - - -
285I ASP* 2.4 44.4 - - - +
286I GLU* 2.2 34.9 + - - +
287I ILE* 3.9 1.1 - - - +
329I MET* 1.3 73.9 - - - +
331I THR* 1.3 58.6 + - - +
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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