Contacts of the strand formed by residues 313 - 320 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291I ASN* 4.6 2.4 + - - +
311I GLY 3.7 4.9 + - - +
312I THR* 1.3 82.6 - - - +
314I VAL* 1.3 61.2 + - - +
328I GLU* 3.6 38.5 + - + +
329I VAL 3.3 5.2 - - - +
330I THR* 3.4 30.0 + - - +
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Residues in contact with VAL 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I LEU* 4.2 3.6 - - + -
290I LEU* 3.8 10.3 - - + -
291I ASN* 3.5 17.5 - - - +
305I ILE* 4.0 18.6 - - + -
308I THR* 4.6 12.8 - - + +
312I THR* 4.7 2.0 - - + +
313I LYS* 1.3 77.3 - - - +
315I LYS* 1.3 60.8 + - - +
316I LEU* 3.9 21.3 + - + -
327I VAL 3.6 1.4 - - - +
328I GLU* 3.3 4.8 - - - -
329I VAL* 2.8 41.4 + - + +
331I LEU* 4.0 30.5 - - + -
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Residues in contact with LYS 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C SER* 5.1 10.7 + - - +
290I LEU* 3.5 6.9 - - - +
291I ASN* 2.8 49.6 + - - +
314I VAL* 1.3 75.0 - - - +
316I LEU* 1.3 61.6 + - - +
317I GLY 4.0 0.7 + - - -
326I GLU* 3.4 29.5 - - - +
327I VAL 3.4 4.0 - - - +
328I GLU* 3.5 33.6 + - + +
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Residues in contact with LEU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I LEU* 4.1 19.7 - - + -
244I ILE* 5.7 0.4 - - + -
276I SER* 5.0 1.3 - - - +
281I VAL* 4.4 13.9 - - + -
287I ILE* 3.9 39.0 - - + -
289I SER 3.6 3.1 - - - +
290I LEU* 3.9 25.6 - - + -
301I LEU* 5.1 1.1 - - + -
314I VAL* 3.9 17.0 - - + -
315I LYS* 1.3 69.9 - - - +
317I GLY* 1.3 61.9 + - - +
318I LEU* 3.3 11.2 + - + +
325I LEU 3.5 0.2 - - - +
326I GLU* 3.4 6.6 - - - -
327I VAL* 2.7 40.8 + - + +
329I VAL* 3.8 20.0 - - + -
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Residues in contact with GLY 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287I ILE* 3.3 7.5 - - - +
288I THR* 2.6 35.6 + - - -
289I SER* 2.9 31.8 + - - -
316I LEU* 1.3 67.2 - - - +
318I LEU* 1.3 55.4 + - - -
325I LEU 3.9 4.0 - - - -
326I GLU* 3.9 12.1 + - - -
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Residues in contact with LEU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281I VAL* 4.0 22.0 - - + -
285I ASP* 3.3 41.1 - - + +
286I ILE 3.5 8.7 - - - +
287I ILE* 4.5 7.0 - - + +
288I THR* 4.9 2.2 + - - -
316I LEU* 3.9 11.7 - - + +
317I GLY* 1.3 73.4 - - - -
319I LEU* 1.3 76.1 + - - +
320I ARG* 4.1 7.2 - - - +
324I PRO* 3.6 5.9 - - - +
325I LEU* 2.9 61.4 + - + +
327I VAL* 4.2 18.4 - - + -
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Residues in contact with LEU 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259I LEU* 4.1 29.6 - - + -
260I ASP 5.6 1.3 - - - +
261I VAL* 3.8 28.0 - - + -
284I GLY 4.4 1.2 - - - +
285I ASP* 3.9 1.9 - - - -
286I ILE* 3.0 44.1 + - + +
288I THR* 4.5 8.3 - - + +
318I LEU* 1.3 83.9 - - - +
320I ARG* 1.4 59.7 + - - +
321I ASN 4.3 0.9 + - - -
322I GLY* 4.2 16.3 + - - +
323I LYS 3.5 2.5 - - - -
324I PRO* 3.9 27.4 - - + -
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Residues in contact with ARG 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280I GLY 2.7 29.2 + - - -
281I VAL* 3.7 2.6 - - - +
282I LYS* 3.6 25.7 - - - +
284I GLY 5.4 2.2 - - - +
285I ASP* 3.0 42.5 + - - +
318I LEU* 4.1 7.6 - - + +
319I LEU* 1.4 71.5 - - - +
321I ASN* 1.3 73.4 + - + +
322I GLY 3.1 0.7 - - - -
323I LYS* 2.9 31.1 + - + +
325I LEU* 3.7 31.5 - - + +
327I VAL* 5.3 3.2 - - - +
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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