Contacts of the strand formed by residues 323 - 330 (chain C) in PDB entry 3STJ
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 LYS 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319C LEU* 3.5 4.1 - - - -
320C ARG* 3.0 33.4 + - + +
321C ASN* 3.8 19.5 - - + +
322C GLY* 1.3 83.3 + - - +
324C PRO* 1.3 75.8 - - + +
325C LEU* 3.7 7.6 + - + +
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Residues in contact with PRO 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LEU 3.6 9.4 - - - +
319C LEU* 3.8 12.8 - - + -
322C GLY 4.1 4.5 - - - +
323C LYS* 1.3 90.9 - - + +
325C LEU* 1.3 70.0 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C GLY* 3.8 2.6 - - - -
318C LEU* 2.9 47.1 + - + +
320C ARG* 3.6 50.5 - - + +
323C LYS* 4.2 10.1 - - + +
324C PRO* 1.3 82.9 - - - +
326C GLU* 1.3 62.2 + - - +
327C VAL* 4.7 9.9 - - + -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C SER* 5.2 1.0 - - - -
292C GLY* 4.5 12.5 + - - -
315C LYS* 3.4 45.9 - - - +
316C LEU 3.4 3.8 - - - +
317C GLY* 3.9 18.4 + - - -
325C LEU* 1.3 73.9 - - - +
327C VAL* 1.3 65.8 + - - +
328C GLU 4.3 0.2 - - - -
123I LYS* 5.0 17.1 + - - -
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C ALA* 3.6 39.7 - - + +
280C GLY 5.3 0.4 - - - +
281C VAL* 4.0 12.3 - - + +
314C VAL 3.5 0.7 - - - +
315C LYS* 3.5 3.6 - - - -
316C LEU* 2.7 44.3 + - + +
318C LEU* 4.2 22.0 - - + -
320C ARG* 5.2 6.5 - - - +
325C LEU* 4.7 13.5 - - + -
326C GLU* 1.3 79.1 - - - +
328C GLU* 1.3 61.7 + - - +
329C VAL* 3.8 11.3 + - + -
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Residues in contact with GLU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C ALA* 3.2 18.0 - - - +
313C LYS* 3.6 38.1 + - + +
314C VAL 3.2 10.3 - - - +
315C LYS* 3.5 22.7 - - + +
326C GLU 4.3 0.2 - - - -
327C VAL* 1.3 73.1 - - - +
329C VAL* 1.3 59.7 + - - +
330C THR 4.5 0.2 + - - -
122I SER* 3.4 13.0 + - - -
123I LYS* 3.0 46.2 + - + +
124I LEU 4.3 3.3 + - - +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C LEU* 3.8 26.7 - - + +
275C GLY 3.5 24.5 - - - -
276C SER* 3.5 4.5 - - - +
279C ALA* 4.0 8.1 - - + -
281C VAL* 4.1 7.4 - - + -
312C THR 3.6 0.7 - - - +
313C LYS* 3.2 3.6 - - - -
314C VAL* 2.8 38.3 + - + +
316C LEU* 3.8 27.6 - - + -
327C VAL* 3.8 17.7 - - + +
328C GLU* 1.3 76.4 - - - +
330C THR* 1.3 71.0 + - - +
331C LEU* 4.8 1.1 - - + -
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Residues in contact with THR 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LEU 4.8 0.2 - - - +
275C GLY* 3.4 27.7 + - - -
311C GLY* 3.5 30.7 - - - +
312C THR 3.6 3.8 - - - +
313C LYS* 3.4 29.4 + - + +
328C GLU 4.4 0.4 - - - -
329C VAL* 1.3 74.7 - - - +
331C LEU* 1.3 66.1 + - - +
332C ASP* 3.6 2.9 + - - +
73I SER 6.0 0.2 - - - +
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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