Contacts of the helix formed by residues 317 - 330 (chain B) in PDB entry 3N9V
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 PRO 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B ASP* 4.5 4.7 - - - +
316B THR* 1.3 89.1 - - - +
318B LYS* 1.3 64.7 + - + +
319B GLU 3.3 0.6 + - - -
320B GLU* 3.6 9.5 + - + +
321B GLU* 3.3 35.2 + - - +
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Residues in contact with LYS 318 (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 GLY 3.5 20.9 - - - +
277B GLN 4.3 5.8 - - - +
278B SER* 3.2 28.8 + - - +
304B LEU* 3.3 33.8 - - + +
305B ASP* 4.1 18.1 + - + +
316B THR* 3.0 9.2 + - - +
317B PRO* 1.3 84.0 - - + +
319B GLU* 1.3 63.8 + - - +
321B GLU* 3.1 22.4 + - - +
322B TRP* 3.1 31.0 + - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.7 12.4 - - - +
314B HIS* 4.5 3.5 + - - -
316B THR* 3.4 14.6 + - - +
317B PRO 3.3 0.8 - - - -
318B LYS* 1.3 78.3 - - - +
320B GLU* 1.3 60.9 + - + +
323B PHE* 3.0 29.5 + - + +
341B LEU* 3.8 39.4 - - + +
343B ARG* 2.7 46.0 + - - +
348B MET* 4.0 8.4 - - - +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR 4.6 0.2 + - - -
317B PRO* 3.6 10.9 + - + +
319B GLU* 1.3 79.7 - - + +
321B GLU* 1.3 67.8 - - + +
323B PHE* 3.8 11.8 - - - +
324B LYS* 3.0 43.0 + - + +
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Residues in contact with GLU 321 (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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278B SER* 2.6 34.8 + - - -
279B PRO* 3.7 16.8 - - + +
317B PRO* 3.3 27.0 + - - +
318B LYS* 3.1 25.9 + - - +
319B GLU 3.3 0.4 - - - -
320B GLU* 1.3 80.6 - - + +
322B TRP* 1.3 57.5 + - - +
324B LYS* 3.8 4.5 - - - +
325B ALA* 3.0 24.8 + - - +
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Residues in contact with TRP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B TYR* 4.2 10.8 - + - -
274B VAL* 3.4 36.4 - - + +
277B GLN 2.8 30.0 + - - -
278B SER* 3.7 3.3 - - - +
279B PRO* 3.4 42.1 - - + +
283B LEU* 4.0 27.8 - - + -
301B PHE* 3.5 25.1 - + + -
304B LEU* 3.6 19.1 + - + +
318B LYS* 3.1 27.8 + - + +
321B GLU* 1.3 77.2 - - - +
323B PHE* 1.3 56.3 + - - +
325B ALA* 3.4 2.3 - - + +
326B VAL* 2.7 41.2 + - - +
348B MET* 4.1 16.6 - - + -
546B THR* 4.6 10.5 - - + -
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Residues in contact with PHE 323 (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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426A GLN 5.8 1.6 - - - -
429A PRO* 4.6 16.6 - - + -
319B GLU* 3.0 19.7 + - + +
320B GLU* 3.8 13.2 - - - +
322B TRP* 1.3 77.5 - - - +
324B LYS* 1.3 67.0 + - + +
326B VAL 3.5 0.2 + - - -
327B SER* 3.0 45.2 + - - -
338B LYS* 3.5 44.9 - - + -
341B LEU* 4.4 11.0 - - + -
348B MET* 4.4 2.1 - - + +
350B LEU* 3.6 28.9 - - + -
352B TYR* 3.4 22.8 + + - -
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Residues in contact with LYS 324 (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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429A PRO 6.1 0.7 - - - +
320B GLU* 3.0 38.9 + - + +
321B GLU* 3.8 4.7 - - - +
323B PHE* 1.3 79.6 - - + +
325B ALA* 1.3 65.0 + - - +
327B SER* 3.4 5.6 + - - -
328B GLU* 3.0 42.9 + - + +
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Residues in contact with ALA 325 (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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279B PRO* 3.8 24.0 - - + -
281B GLU 5.5 2.0 - - - +
283B LEU* 3.7 26.3 + - + +
321B GLU 3.0 15.8 + - - +
322B TRP* 3.0 9.6 + - - +
324B LYS* 1.3 77.0 - - - +
326B VAL* 1.3 62.4 + - - +
328B GLU* 3.3 12.3 + - - +
329B GLY* 3.0 18.7 + - - -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.9 8.5 - - + -
287B LEU* 3.6 14.3 - - + +
299B VAL* 4.3 13.7 - - + -
301B PHE* 3.4 34.3 - - + -
322B TRP 2.7 23.7 + - - +
323B PHE 3.8 0.4 - - - +
325B ALA* 1.3 70.4 - - - +
327B SER* 1.3 65.4 + - - +
329B GLY* 2.9 11.3 + - - -
330B LEU* 3.0 22.2 + - + +
350B LEU* 4.0 7.2 - - + -
352B TYR* 3.3 35.7 - - + +
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Residues in contact with SER 327 (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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429A PRO* 4.0 18.9 - - - +
323B PHE* 3.0 26.9 + - - -
324B LYS* 3.7 7.0 - - - -
325B ALA 3.3 0.2 - - - -
326B VAL* 1.3 77.6 - - - +
328B GLU* 1.3 62.8 + - - +
329B GLY 3.3 0.3 + - - -
330B LEU* 3.4 25.0 + - - +
352B TYR* 3.0 29.0 + - - -
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Residues in contact with GLU 328 (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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282B CYS* 5.7 1.8 - - - -
284B ARG* 4.1 10.6 - - - +
324B LYS* 3.0 31.3 + - + +
325B ALA* 3.7 9.3 - - - +
327B SER* 1.3 76.3 - - - +
329B GLY* 1.3 57.9 + - - +
330B LEU 3.6 2.5 - - - +
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Residues in contact with GLY 329 (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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282B CYS* 5.6 0.4 - - - -
283B LEU* 4.4 2.7 - - - -
284B ARG* 3.6 22.8 - - - -
287B LEU* 3.4 21.4 - - - +
288B SER* 2.8 23.2 + - - -
325B ALA 3.0 9.7 + - - -
326B VAL 2.9 8.0 + - - -
328B GLU* 1.3 76.6 - - - +
330B LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 330 (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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429A PRO* 6.5 0.9 - - + -
284B ARG* 4.4 2.1 - - - -
287B LEU* 4.6 4.5 - - + -
297B TYR* 3.5 39.9 - - + -
299B VAL* 5.1 0.2 - - + -
326B VAL* 3.0 33.8 + - + +
327B SER* 3.4 15.3 + - - +
328B GLU 4.4 4.5 - - - +
329B GLY* 1.3 81.1 - - - +
331B HIS* 1.3 65.7 + - - +
332B PRO* 3.2 7.8 - - - +
336B TYR* 3.7 33.2 - - + -
352B TYR* 3.5 37.2 - - + -
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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