Contacts of the helix formed by residues 301 - 313 (chain B) in PDB entry 5V8V
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 SER 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLY* 1.3 76.1 - - - +
302B THR* 1.3 64.1 + - - +
303B SER* 3.4 9.1 + - - -
304B SER* 3.0 30.0 + - - -
305B ILE* 2.9 22.5 + - - +
369B MET 4.1 3.7 + - - -
370B ASP* 3.4 15.9 - - - +
377B PRO* 5.3 12.6 - - - -
378B THR 4.5 7.8 + - - -
379B TRP* 5.3 1.8 - - - +
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Residues in contact with THR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LYS* 5.8 2.9 - - - +
300B GLY 3.7 0.8 + - - -
301B SER* 1.3 72.8 - - - +
303B SER* 1.3 62.0 + - - +
305B ILE* 4.1 0.5 - - - +
306B GLU* 3.1 43.1 + - + +
368B ALA* 3.7 24.0 - - + +
370B ASP* 2.7 30.2 + - - -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 5.3 2.3 - - - +
301B SER* 3.1 8.2 + - - -
302B THR* 1.3 81.4 - - - +
304B SER* 1.3 65.1 + - - +
306B GLU* 3.3 9.3 + - - +
307B LYS* 3.3 20.3 + - - +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.2 33.4 - - - +
283B CYS 5.6 0.5 + - - -
301B SER* 3.0 23.2 + - - -
303B SER* 1.3 76.7 + - - +
305B ILE* 1.3 60.0 + - - +
307B LYS 3.2 1.9 + - - -
308B LEU* 2.9 24.9 + - - +
379B TRP* 3.6 34.7 + - - -
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Residues in contact with ILE 305 (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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300B GLY* 3.8 17.7 - - - +
301B SER 2.9 19.9 + - - +
302B THR 4.3 1.1 - - - +
304B SER* 1.3 72.8 - - - +
306B GLU* 1.3 60.2 + - - +
308B LEU* 4.3 7.6 - - + +
309B MET* 2.8 42.9 + - + +
321B TYR* 3.6 31.6 - - + +
366B ILE* 4.0 19.3 - - + -
367B HIS 3.8 15.9 - - - +
368B ALA* 3.8 20.9 - - + +
379B TRP* 4.0 21.1 - - + -
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 5.8 4.6 - - - +
302B THR* 3.1 39.9 + - + +
303B SER* 3.4 8.1 - - - +
305B ILE* 1.3 76.5 - - - +
307B LYS* 1.3 61.1 + - - +
309B MET* 4.2 1.7 - - - +
310B GLU* 3.2 26.8 + - - +
321B TYR* 4.5 14.8 + - - +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 2.4 49.9 + - + +
282B LEU* 4.1 14.1 - - + +
303B SER 3.3 7.5 + - - +
304B SER 3.2 7.9 + - - +
306B GLU* 1.3 76.9 - - - +
308B LEU* 1.3 64.2 - - - +
310B GLU* 3.5 11.1 + - - +
311B ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 308 (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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274B VAL* 5.3 2.7 - - + -
276B VAL* 3.5 29.4 - - + -
281B LEU* 4.1 11.2 - - + -
282B LEU* 4.1 9.3 - - + +
304B SER 2.9 16.1 + - - +
305B ILE* 3.9 20.9 - - + +
307B LYS* 1.3 78.3 - - - +
309B MET* 1.3 62.2 + - + +
311B ALA* 3.1 5.4 + - - +
312B LEU* 3.0 39.5 + - + +
334B ILE* 4.0 37.0 - - + -
336B PHE* 6.5 0.2 - - + -
366B ILE* 4.5 17.0 - - + -
379B TRP* 4.7 10.1 - - + -
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 2.8 29.4 + - + +
306B GLU 4.3 1.8 - - - +
308B LEU* 1.3 70.8 - - + +
310B GLU* 1.3 67.2 + - - +
312B LEU* 3.0 9.4 + - + +
313B GLY 3.0 18.7 + - - -
314B ALA* 3.2 20.7 + - - +
321B TYR* 3.4 62.6 - - + -
364B LEU* 3.6 28.5 - - + -
366B ILE* 3.8 40.2 - - + +
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Residues in contact with GLU 310 (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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306B GLU 3.2 20.4 + - - +
307B LYS* 3.7 10.7 - - - +
309B MET* 1.3 76.3 - - - +
311B ALA* 1.3 61.8 + - - +
313B GLY* 3.3 11.9 + - - +
314B ALA 5.2 1.6 - - - -
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Residues in contact with ALA 311 (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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276B VAL* 4.3 19.7 - - + +
281B LEU* 3.8 19.7 - - + -
307B LYS 3.1 12.2 + - - +
308B LEU 3.1 10.1 + - - +
310B GLU* 1.3 79.5 - - - +
312B LEU* 1.3 61.1 + - - +
313B GLY 3.5 0.3 + - - -
332B PRO* 5.1 3.6 - - - +
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Residues in contact with LEU 312 (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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276B VAL* 4.4 9.2 - - + -
308B LEU* 3.0 24.7 + - + +
309B MET* 3.0 17.9 + - + +
311B ALA* 1.3 77.6 - - - +
313B GLY* 1.3 61.0 + - - +
314B ALA* 4.1 7.4 - - + +
323B VAL* 4.7 0.5 - - - +
331B LEU* 3.2 28.0 - - + +
332B PRO* 4.1 22.6 - - + +
334B ILE* 4.0 26.5 - - + -
350B TYR* 3.9 20.9 - - + +
364B LEU* 3.6 27.4 - - + -
366B ILE* 5.0 0.7 - - + -
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Residues in contact with GLY 313 (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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309B MET 3.0 5.1 + - - -
310B GLU* 3.3 8.0 + - - -
311B ALA 3.3 4.2 + - - -
312B LEU* 1.3 78.8 - - - +
314B ALA* 1.3 61.8 + - - +
315B LYS* 3.9 14.5 + - - +
322B VAL 4.7 0.5 - - - +
323B VAL* 4.5 6.9 - - - +
327B GLU* 5.4 3.3 - - - +
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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