Contacts of the strand formed by residues 313 - 320 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ASN* 4.7 1.9 + - - +
311B GLY 4.4 1.3 - - - +
312B THR* 1.3 81.7 - - - +
314B VAL* 1.3 63.7 + - - +
328B GLU* 3.6 37.1 + - + +
329B VAL 3.2 4.5 - - - +
330B THR* 3.4 30.3 - - - +
72E ALA 5.0 2.7 - - - +
73E SER* 3.3 41.5 + - - +
121E PRO* 2.5 41.8 + - - +
122E SER* 4.0 0.8 - - - +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.2 10.1 - - + -
290B LEU* 3.7 27.4 - - + -
291B ASN* 3.5 15.0 - - - +
305B ILE* 4.1 8.5 - - + -
308B THR* 4.6 13.0 - - + +
312B THR* 4.7 1.3 - - + +
313B LYS* 1.3 78.9 - - - +
315B LYS* 1.3 60.8 + - - +
316B LEU* 3.9 4.2 + - + -
327B VAL 3.6 0.9 - - - +
328B GLU* 3.2 5.3 - - - +
329B VAL* 2.8 44.1 + - + +
331B LEU* 4.0 35.2 - - + -
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.5 6.6 - - - +
291B ASN* 2.7 49.9 + - - +
314B VAL* 1.3 73.2 - - - +
316B LEU* 1.3 61.7 + - - +
317B GLY 4.0 0.3 + - - -
326B GLU* 3.4 30.4 - - - +
327B VAL 3.4 7.0 - - - +
328B GLU* 3.6 30.0 + - + +
123E LYS* 4.5 25.2 - - - +
124E LEU 5.4 3.0 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.8 22.7 - - + -
244B ILE* 5.8 0.2 - - + -
276B SER* 4.9 0.9 - - - +
281B VAL* 4.4 13.5 - - + -
287B ILE* 3.9 31.4 - - + -
289B SER 3.6 4.9 - - - +
290B LEU* 3.7 27.6 - - + -
301B LEU* 4.7 3.1 - - + -
314B VAL* 3.9 8.9 + - + -
315B LYS* 1.3 71.9 - - - +
317B GLY* 1.3 61.0 + - - +
318B LEU* 3.6 10.6 + - + +
325B LEU 3.7 0.3 - - - +
326B GLU* 3.5 7.3 - - - -
327B VAL* 2.7 38.9 + - + +
329B VAL* 3.5 26.0 - - + -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 3.2 8.8 - - - +
288B THR* 2.7 33.5 + - - -
289B SER* 2.8 33.7 + - - -
315B LYS 4.0 1.0 + - - -
316B LEU* 1.3 69.7 - - - +
318B LEU* 1.3 55.6 + - - -
325B LEU 3.8 4.7 - - - -
326B GLU* 4.0 9.5 + - - -
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Residues in contact with LEU 318 (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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281B VAL* 4.3 21.1 - - + -
285B ASP* 3.1 37.2 - - + +
286B ILE 3.4 6.3 - - - +
287B ILE* 4.3 16.6 - - + -
288B THR* 4.9 2.9 - - - -
316B LEU* 4.3 15.7 - - + +
317B GLY* 1.3 75.5 - - - -
319B LEU* 1.3 64.3 - - - +
320B ARG* 3.4 16.2 - - + +
324B PRO* 3.4 6.8 - - - +
325B LEU* 2.9 57.7 + - + +
327B VAL* 4.8 8.7 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 4.3 20.9 - - + -
260B ASP 5.7 1.1 - - - +
261B VAL* 3.4 33.0 - - + -
284B GLY 4.4 2.1 - - - +
285B ASP* 3.5 6.8 - - - -
286B ILE* 2.9 42.4 + - + +
288B THR* 4.4 6.5 - - + +
318B LEU* 1.3 77.0 - - - +
320B ARG* 1.3 58.7 + - - +
321B ASN 4.1 1.8 + - - -
322B GLY* 4.1 18.2 - - - +
323B LYS 3.4 21.3 - - - -
324B PRO* 3.7 15.9 - - + -
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Residues in contact with ARG 320 (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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280B GLY 2.7 29.7 + - - -
281B VAL* 3.8 0.6 - - - +
282B LYS* 3.6 29.2 - - - +
284B GLY 5.6 0.9 - - - -
285B ASP* 2.7 40.1 + - - +
318B LEU* 3.4 10.9 - - - +
319B LEU* 1.3 72.3 - - - +
321B ASN* 1.3 79.2 + - - +
323B LYS* 2.8 28.8 + - - +
325B LEU* 3.6 32.4 - - + +
327B VAL* 5.2 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