Contacts of the strand formed by residues 313 - 320 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L ASN* 4.6 2.4 + - - +
311L GLY 3.7 3.3 + - - +
312L THR* 1.3 81.3 - - - +
314L VAL* 1.3 63.5 + - - +
328L GLU* 3.6 38.1 + - + +
329L VAL 3.3 4.7 - - - +
330L THR* 3.4 31.6 + - + +
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Residues in contact with VAL 314 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L LEU* 4.2 4.3 - - + -
290L LEU* 3.8 14.4 - - + -
291L ASN* 3.5 17.5 - - - +
305L ILE* 4.0 9.2 - - + -
308L THR* 4.6 13.7 - - + +
312L THR* 4.7 2.0 - - + -
313L LYS* 1.3 78.2 - - - +
315L LYS* 1.3 62.2 + - - +
316L LEU* 3.9 20.4 - - + -
327L VAL 3.6 1.0 - - - +
328L GLU* 3.3 4.5 - - - -
329L VAL* 2.8 42.7 + - + +
331L LEU* 4.0 34.5 - - + -
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Residues in contact with LYS 315 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H SER* 5.6 9.1 - - - +
122H SER* 6.4 0.4 - - - +
123H LYS 6.1 0.6 - - - +
290L LEU* 3.5 7.4 - - - +
291L ASN* 2.7 48.4 + - - +
292L GLY 5.2 0.2 - - - +
314L VAL* 1.3 75.5 - - - +
316L LEU* 1.3 60.9 + - - +
317L GLY 4.0 0.3 + - - -
326L GLU* 3.4 29.7 - - - +
327L VAL 3.5 4.0 - - - +
328L GLU* 3.5 34.0 + - + +
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Residues in contact with LEU 316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L LEU* 4.1 20.4 - - + -
244L ILE* 5.7 0.2 - - + -
276L SER* 5.0 1.1 - - - +
281L VAL* 4.2 14.8 - - + -
287L ILE* 3.9 39.0 - - + -
289L SER 3.6 3.1 - - - +
290L LEU* 3.8 25.1 - - + -
301L LEU* 5.1 1.1 - - + -
314L VAL* 3.9 17.0 - - + -
315L LYS* 1.3 70.0 - - - +
317L GLY* 1.3 63.4 + - - +
318L LEU* 3.3 10.5 + - + +
325L LEU 3.5 0.3 - - - +
326L GLU* 3.4 6.6 - - - -
327L VAL* 2.7 39.8 + - + +
329L VAL* 3.8 20.4 - - + -
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Residues in contact with GLY 317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287L ILE* 3.3 7.7 - - - +
288L THR* 2.6 35.4 + - - -
289L SER* 2.9 32.7 + - - -
316L LEU* 1.3 68.0 - - - +
318L LEU* 1.3 55.6 + - - -
325L LEU 3.9 3.4 - - - -
326L GLU* 3.9 12.2 + - - -
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Residues in contact with LEU 318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L VAL* 4.2 19.7 - - + -
285L ASP* 3.4 39.9 - - + +
286L ILE 3.5 8.7 - - - +
287L ILE* 4.5 6.5 - - + +
288L THR* 4.9 2.2 + - - -
316L LEU* 3.9 11.0 - - + +
317L GLY* 1.3 74.4 - - - -
319L LEU* 1.3 75.7 + - - +
320L ARG* 4.0 8.1 - - - +
324L PRO* 3.6 6.1 - - - +
325L LEU* 2.9 62.9 + - + +
327L VAL* 4.2 22.4 - - + -
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Residues in contact with LEU 319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L LEU* 4.1 29.6 - - + -
260L ASP 5.6 1.3 - - - +
261L VAL* 3.8 27.4 - - + -
284L GLY 4.4 0.9 - - - +
285L ASP* 3.9 2.3 - - - -
286L ILE* 3.1 44.9 + - + +
288L THR* 4.5 8.7 - - + +
318L LEU* 1.3 83.9 - - - +
320L ARG* 1.4 61.1 + - - +
321L ASN 4.3 0.3 + - - -
322L GLY* 4.2 16.1 + - - +
323L LYS 3.5 3.4 - - - -
324L PRO* 3.8 27.1 - - + -
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Residues in contact with ARG 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L GLY 2.7 30.6 + - - -
281L VAL* 4.0 1.0 - - - +
282L LYS* 3.6 30.0 - - - +
284L GLY 5.4 2.5 - - - +
285L ASP* 3.0 42.7 + - - +
318L LEU* 4.0 9.4 - - + +
319L LEU* 1.4 71.2 - - - +
321L ASN* 1.3 72.9 + - + +
322L GLY 3.1 0.7 - - - -
323L LYS* 2.9 31.3 + - + +
325L LEU* 3.7 31.9 - - + +
327L VAL* 5.3 3.0 - - - +
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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