Contacts of the strand formed by residues 313 - 320 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ASN* 4.6 2.4 + - - +
311D GLY 3.7 3.3 + - - +
312D THR* 1.3 81.3 - - - +
314D VAL* 1.3 62.4 + - - +
328D GLU* 3.6 38.9 + - + +
329D VAL 3.3 5.2 - - - +
330D THR* 3.4 31.4 + - + +
120G ASN* 3.2 33.3 + - - +
121G PRO 4.9 13.8 + - - +
122G SER* 6.0 3.1 - - - -
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LEU* 4.2 5.6 - - + -
290D LEU* 3.8 16.6 - - + -
291D ASN* 3.4 17.5 - - - +
305D ILE* 4.4 4.9 - - + -
308D THR* 4.6 13.0 - - + +
312D THR* 4.7 1.3 - - + -
313D LYS* 1.3 78.6 - - - +
315D LYS* 1.3 62.2 + - - +
316D LEU* 3.9 21.5 + - + -
327D VAL 3.6 0.9 - - - +
328D GLU* 3.3 4.9 - - - -
329D VAL* 2.8 41.9 + - + +
331D LEU* 4.0 35.7 - - + -
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Residues in contact with LYS 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D LEU* 3.4 7.4 - - - +
291D ASN* 2.7 50.3 + - - +
314D VAL* 1.3 74.1 - - - +
316D LEU* 1.3 60.0 + - - +
317D GLY 4.0 0.5 + - - -
326D GLU* 3.4 29.7 - - - +
327D VAL 3.5 3.6 - - - +
328D GLU* 3.5 33.8 + - + +
123G LYS* 3.4 41.1 - - - +
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LEU* 4.1 19.7 - - + -
244D ILE* 5.7 0.2 - - + -
276D SER* 5.0 1.3 - - - +
281D VAL* 4.2 14.8 - - + -
287D ILE* 3.9 37.2 - - + -
289D SER 3.6 2.9 - - - +
290D LEU* 3.8 25.1 - - + -
301D LEU* 5.1 1.3 - - + -
314D VAL* 3.9 17.0 - - + -
315D LYS* 1.3 70.7 - - - +
317D GLY* 1.3 63.2 + - - +
318D LEU* 3.3 10.9 + - + +
325D LEU 3.6 0.3 - - - +
326D GLU* 3.4 6.7 - - - -
327D VAL* 2.7 40.9 + - + +
329D VAL* 3.8 20.2 - - + -
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Residues in contact with GLY 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ILE* 3.3 8.0 - - - +
288D THR* 2.6 35.0 + - - -
289D SER* 2.9 32.1 + - - -
315D LYS 4.0 0.2 + - - -
316D LEU* 1.3 68.5 - - - +
318D LEU* 1.3 55.2 + - - -
325D LEU 3.9 4.5 - - - -
326D GLU* 3.9 11.9 + - - -
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D VAL* 4.2 20.6 - - + -
285D ASP* 3.4 40.4 - - + +
286D ILE 3.5 8.5 - - - +
287D ILE* 4.9 6.3 - - + -
288D THR* 4.9 2.0 + - - -
316D LEU* 3.9 11.4 - - + +
317D GLY* 1.3 74.3 - - - -
319D LEU* 1.3 76.5 + - - +
320D ARG* 4.1 8.3 - - - +
324D PRO* 3.6 5.7 - - - +
325D LEU* 2.9 62.3 + - + +
327D VAL* 4.2 20.4 - - + -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D LEU* 4.0 30.1 - - + -
260D ASP 5.6 1.3 - - - +
261D VAL* 3.8 27.1 - - + -
284D GLY 4.4 0.9 - - - +
285D ASP* 3.9 2.3 - - - -
286D ILE* 3.0 43.8 + - + +
288D THR* 4.5 7.9 - - + +
318D LEU* 1.3 83.6 - - - +
320D ARG* 1.4 59.2 + - - +
321D ASN 4.2 0.7 + - - -
322D GLY* 4.2 13.6 + - - +
323D LYS 3.5 5.2 - - - +
324D PRO* 3.8 28.3 - - + -
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Residues in contact with ARG 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D GLY 2.6 30.7 + - - -
281D VAL* 4.0 0.8 - - - +
282D LYS* 3.7 28.3 - - - +
284D GLY 5.4 2.0 - - - +
285D ASP* 3.0 43.2 + - - +
318D LEU* 4.1 8.3 - - + +
319D LEU* 1.4 70.6 - - - +
321D ASN* 1.3 70.8 + - + +
322D GLY 3.1 0.9 - - - -
323D LYS* 2.9 33.5 + - + +
325D LEU* 3.7 31.3 - - + +
327D VAL* 5.3 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