Contacts of the strand formed by residues 313 - 320 (chain G) 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 313 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN* 3.9 28.8 - - - +
121D PRO 6.0 1.6 - - - +
291G ASN* 4.6 1.9 + - - +
311G GLY 3.7 4.7 + - - +
312G THR* 1.3 81.2 - - - +
314G VAL* 1.4 63.9 + - - +
328G GLU* 3.6 38.1 + - + +
329G VAL 3.3 4.7 - - - +
330G THR* 3.4 29.5 + - - +
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Residues in contact with VAL 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G LEU* 4.2 6.3 - - + -
290G LEU* 3.7 17.9 - - + -
291G ASN* 3.5 17.7 - - - +
305G ILE* 4.2 4.9 - - + -
308G THR* 4.6 12.8 - - + +
312G THR* 4.7 2.2 - - + +
313G LYS* 1.4 78.1 - - - +
315G LYS* 1.3 62.5 + - - +
316G LEU* 3.9 21.5 + - + -
327G VAL 3.6 0.9 - - - +
328G GLU* 3.3 4.3 - - - -
329G VAL* 2.8 40.8 + - + +
331G LEU* 4.0 36.1 - - + -
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Residues in contact with LYS 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D SER* 5.3 4.4 + - - -
123D LYS* 4.3 26.5 - - - +
290G LEU* 3.5 7.4 - - - +
291G ASN* 2.7 49.7 + - - +
292G GLY 5.2 0.2 - - - +
314G VAL* 1.3 73.7 - - - +
316G LEU* 1.3 61.1 + - - +
317G GLY 4.0 0.5 + - - -
326G GLU* 3.4 29.0 - - - +
327G VAL 3.5 4.5 - - - +
328G GLU* 3.5 33.7 - - + +
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Residues in contact with LEU 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G LEU* 4.1 18.8 - - + -
276G SER* 5.0 0.9 - - - +
281G VAL* 4.2 15.3 - - + -
287G ILE* 3.9 39.5 - - + -
289G SER 3.6 2.9 - - - +
290G LEU* 3.8 25.6 - - + -
301G LEU* 5.1 0.9 - - + -
314G VAL* 3.9 16.8 - - + -
315G LYS* 1.3 70.5 - - - +
317G GLY* 1.3 61.4 + - - +
318G LEU* 3.4 10.6 + - + +
325G LEU 3.5 0.2 - - - +
326G GLU* 3.4 7.0 - - - -
327G VAL* 2.7 39.5 + - + +
329G VAL* 3.8 20.0 - - + -
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Residues in contact with GLY 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G ILE* 3.2 7.3 - - - +
288G THR* 2.6 35.0 + - - -
289G SER* 2.9 31.0 + - - -
316G LEU* 1.3 68.2 - - - +
318G LEU* 1.3 55.3 + - - -
325G LEU 3.9 4.5 - - - -
326G GLU* 3.9 11.7 + - - -
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G VAL* 4.2 18.8 - - + -
285G ASP* 3.4 39.7 - - + +
286G ILE 3.5 8.3 - - - +
287G ILE* 4.9 6.3 - - + -
288G THR* 4.9 2.4 + - - -
316G LEU* 3.9 11.2 - - + +
317G GLY* 1.3 74.0 - - - -
319G LEU* 1.3 75.8 + - - +
320G ARG* 4.0 8.7 - - - +
324G PRO* 3.6 6.6 - - - +
325G LEU* 2.9 59.9 + - + +
327G VAL* 4.2 23.6 - - + -
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Residues in contact with LEU 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259G LEU* 3.9 30.1 - - + -
260G ASP 5.6 1.1 - - - +
261G VAL* 3.9 27.6 - - + -
284G GLY 4.4 0.7 - - - +
285G ASP* 3.9 2.3 - - - -
286G ILE* 3.0 43.9 + - + +
288G THR* 4.5 8.3 - - + +
318G LEU* 1.3 83.4 - - - +
320G ARG* 1.4 60.1 + - - +
321G ASN 4.2 0.9 + - - -
322G GLY* 4.2 12.9 + - - +
323G LYS 3.5 4.9 - - - +
324G PRO* 3.8 27.4 - - + -
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Residues in contact with ARG 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280G GLY 2.6 30.3 + - - -
281G VAL* 4.0 0.8 - - - +
282G LYS* 3.7 29.5 - - - +
284G GLY 5.3 2.5 - - - +
285G ASP* 3.0 43.3 + - - +
318G LEU* 4.0 9.0 - - + +
319G LEU* 1.4 70.5 - - - +
321G ASN* 1.3 69.6 + - + +
322G GLY 3.1 0.7 - - - -
323G LYS* 2.9 34.5 + - + +
325G LEU* 3.7 31.3 - - + +
327G VAL* 5.2 3.4 - - - +
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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