Contacts of the strand formed by residues 309 - 314 (chain D) in PDB entry 2VGB
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 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D ASP 3.1 8.9 + - - +
282D ILE* 3.2 6.5 - - + +
283D VAL 2.8 30.7 + - - -
307D GLY 4.1 7.0 - - - +
308D ILE* 1.3 73.6 - - - +
310D ILE* 1.3 54.8 + - - +
311D ILE* 5.0 0.7 - - + -
331D ASP* 3.2 29.0 + - + +
477D THR 5.0 10.6 + - - -
482D GLN* 4.7 12.1 + - - -
505D GLN* 3.6 38.6 - - + +
508D LEU* 4.0 23.3 - - + -
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Residues in contact with ILE 310 (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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283D VAL* 3.7 8.1 - - + +
285D ALA* 4.9 6.5 - - + -
294D VAL* 4.2 21.8 - - + +
297D VAL* 3.3 37.7 - - + -
298D ARG* 4.1 32.1 - - - +
301D LEU* 4.0 17.5 - - + -
308D ILE 3.9 10.8 - - - +
309D LYS* 1.3 76.0 - - - +
311D ILE* 1.3 62.8 + - - +
312D SER* 4.0 10.7 + - - +
330D SER* 4.1 1.5 - - - -
331D ASP* 2.7 39.7 + - - +
332D GLY 3.5 1.4 + - - -
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Residues in contact with ILE 311 (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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282D ILE* 3.6 24.5 - - + -
283D VAL 2.7 8.3 + - - -
284D PHE* 3.4 29.1 - - + -
285D ALA 2.9 25.9 + - - -
310D ILE* 1.3 77.9 - - - +
312D SER* 1.3 59.8 + - - +
313D LYS 3.4 0.5 + - - -
331D ASP* 4.4 5.4 - - + +
332D GLY* 3.7 23.8 - - - +
333D ILE 3.7 28.9 - - - +
334D MET* 3.7 9.4 - - + +
366D PRO* 4.9 4.5 - - + -
368D VAL* 4.3 6.1 - - + -
508D LEU* 3.9 28.3 - - + -
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Residues in contact with SER 312 (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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285D ALA* 4.0 5.8 - - - +
288D VAL* 3.7 22.3 - - - +
294D VAL* 4.4 7.8 - - - +
310D ILE* 4.0 3.5 - - - +
311D ILE* 1.3 69.8 - - - +
313D LYS* 1.3 62.7 + - - +
314D ILE 3.7 0.5 + - - -
326D ILE* 3.8 18.2 - - - +
330D SER* 2.7 28.7 + - - -
332D GLY 3.1 6.9 + - - -
333D ILE* 3.4 12.9 - - - +
334D MET 2.8 21.9 + - - -
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Residues in contact with LYS 313 (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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156D ASP* 2.6 37.6 + - - +
284D PHE* 3.8 9.0 - - + -
285D ALA 2.9 25.3 + - - +
286D SER* 2.8 19.8 + - - -
287D PHE 4.1 0.9 + - - -
288D VAL* 3.3 28.6 + - - +
311D ILE 4.2 0.4 - - - +
312D SER* 1.3 73.5 - - - +
314D ILE* 1.3 60.8 + - - +
315D GLU* 3.6 15.5 + - + -
334D MET* 3.4 42.0 - - + -
336D ALA* 4.2 7.6 - - + -
581D PGA 3.3 26.4 + - - -
594D K 3.6 4.0 - - - -
595D MN 4.5 0.2 + - - -
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Residues in contact with ILE 314 (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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288D VAL* 3.8 20.6 - - + +
312D SER 4.1 1.3 - - - +
313D LYS* 1.3 73.9 - - - +
315D GLU* 1.3 61.1 + - - +
316D ASN 4.5 0.2 - - - +
319D GLY* 3.9 24.0 - - - +
320D VAL* 3.8 23.8 - - + -
323D PHE* 4.3 4.3 - - + -
326D ILE* 4.0 24.9 - - + -
333D ILE* 4.1 19.5 - - + -
334D MET 2.9 14.5 + - - +
336D ALA* 3.1 22.5 + - - +
340D LEU* 4.1 6.2 - - - +
356D MET* 3.6 33.2 - - + -
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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