Contacts of the strand formed by residues 313 - 320 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H ASN* 4.6 2.3 + - - +
311H GLY 4.5 1.6 - - - +
312H THR* 1.3 82.4 - - - +
314H VAL* 1.3 63.7 + - - +
328H GLU* 3.6 36.2 + - + +
329H VAL 3.3 5.4 - - - +
330H THR* 3.4 29.3 + - - +
72L ALA 4.8 3.1 - - - +
73L SER* 3.4 44.3 + - - +
121L PRO* 2.6 38.6 + - - +
122L SER* 4.2 0.6 - - - +
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Residues in contact with VAL 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H LEU* 4.1 6.7 - - + -
290H LEU* 3.7 20.6 - - + -
291H ASN* 3.5 15.3 - - - +
305H ILE* 4.2 4.5 - - + -
308H THR* 4.6 13.0 - - + +
312H THR* 4.7 1.1 - - + +
313H LYS* 1.3 78.8 - - - +
315H LYS* 1.3 60.6 + - - +
316H LEU* 3.8 21.3 + - + -
327H VAL 3.6 1.0 - - - +
328H GLU* 3.3 5.3 - - - -
329H VAL* 2.8 42.1 + - + +
331H LEU* 4.0 35.0 - - + -
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Residues in contact with LYS 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H LEU* 3.5 7.8 - - - +
291H ASN* 2.8 47.5 + - - +
314H VAL* 1.3 74.4 - - - +
316H LEU* 1.3 60.6 + - - +
317H GLY 4.0 0.7 + - - -
326H GLU* 3.4 29.5 - - - +
327H VAL 3.5 3.6 - - - +
328H GLU* 3.5 32.7 + - + +
123L LYS* 4.7 18.0 - - - +
124L LEU 4.7 11.7 + - - -
125L THR* 5.8 1.6 + - - -
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Residues in contact with LEU 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H LEU* 4.1 19.3 - - + -
244H ILE* 5.7 0.7 - - + -
276H SER* 5.2 1.1 - - - +
281H VAL* 4.3 14.6 - - + -
287H ILE* 3.9 38.4 - - + -
289H SER 3.6 2.9 - - - +
290H LEU* 3.9 15.5 - - + -
301H LEU* 5.1 1.1 - - + -
314H VAL* 3.8 27.1 - - + -
315H LYS* 1.3 70.9 - - - +
317H GLY* 1.3 62.0 + - - +
318H LEU* 3.3 10.3 + - + +
325H LEU 3.5 0.3 - - - +
326H GLU* 3.4 6.2 - - - -
327H VAL* 2.7 40.5 + - + +
329H VAL* 3.9 20.2 - - + -
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Residues in contact with GLY 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H ILE* 3.3 7.6 - - - +
288H THR* 2.6 35.5 + - - -
289H SER* 2.9 31.8 + - - -
316H LEU* 1.3 68.3 - - - +
318H LEU* 1.3 55.8 + - - -
325H LEU 3.9 3.6 - - - -
326H GLU* 3.9 12.6 + - - -
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Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H VAL* 4.2 18.8 - - + -
285H ASP* 3.4 39.7 - - + +
286H ILE 3.5 8.1 - - - +
287H ILE* 4.9 7.0 - - + -
288H THR* 4.9 2.2 + - - -
316H LEU* 3.9 11.9 - - + +
317H GLY* 1.3 73.6 - - - -
319H LEU* 1.3 76.7 + - - +
320H ARG* 4.0 8.5 - - - +
324H PRO* 3.6 6.2 - - - +
325H LEU* 2.9 59.9 + - + +
327H VAL* 4.2 22.2 - - + -
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Residues in contact with LEU 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259H LEU* 4.0 30.7 - - + +
260H ASP 5.5 1.6 - - - +
261H VAL* 3.8 26.7 - - + -
284H GLY 4.4 1.2 - - - +
285H ASP* 3.9 2.3 - - - -
286H ILE* 3.0 43.1 + - + +
288H THR* 4.5 7.9 - - + +
318H LEU* 1.3 83.9 - - - +
320H ARG* 1.4 59.5 + - - +
321H ASN 4.2 0.9 + - - -
322H GLY* 4.2 14.5 + - - +
323H LYS 3.5 5.6 - - - +
324H PRO* 3.8 26.9 - - + -
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Residues in contact with ARG 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280H GLY 2.6 30.5 + - - -
281H VAL* 4.0 1.0 - - - +
282H LYS* 3.7 28.8 - - - +
284H GLY 5.4 2.2 - - - +
285H ASP* 3.0 43.3 + - - +
318H LEU* 4.0 9.0 - - + +
319H LEU* 1.4 71.0 - - - +
321H ASN* 1.3 68.8 + - - +
322H GLY 3.1 0.9 - - - -
323H LYS* 2.9 34.7 + - + +
325H LEU* 3.7 31.9 - - + +
327H VAL* 5.1 3.6 - - - +
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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
------------------------------------------------------------
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