Contacts of the helix formed by residues 308 - 319 (chain B) in PDB entry 6DC0
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 308 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B GLU* 2.7 39.6 + - - -
306B HIS 3.7 3.1 + - - -
307B ILE* 1.3 77.1 - - - +
309B PRO* 1.3 76.0 - - - +
310B LYS* 4.3 3.0 - - - +
311B ALA* 3.2 17.8 + - - +
312B ARG* 2.9 22.5 + - - +
337B TRP* 3.9 2.8 + - - -
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Residues in contact with PRO 309 (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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307B ILE 4.6 0.7 - - - +
308B SER* 1.3 87.1 - - - +
310B LYS* 1.3 63.8 + - + +
312B ARG* 3.3 12.7 + - + +
313B CYS* 3.2 26.8 + - - +
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Residues in contact with LYS 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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290A SER* 5.4 4.9 - - - +
308B SER* 3.4 3.0 + - - +
309B PRO* 1.3 81.0 - - + +
311B ALA* 1.3 61.4 + - - +
313B CYS* 3.7 7.6 + - - -
314B LEU* 3.2 16.5 + - - +
335B HIS* 3.4 16.2 - - + -
336B PRO* 4.3 6.4 - - + +
337B TRP* 4.0 26.0 - - + +
340B SER* 3.3 35.4 - - - +
508B ALA 3.1 26.7 + - - -
509B TYR* 3.3 29.9 + - + +
510B ILE 4.2 0.4 - - - +
511B ASP* 5.2 3.0 + - - -
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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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179B GLU* 3.5 9.2 - - - +
274B LEU* 4.6 1.1 - - + +
278B LEU* 4.0 10.3 - - + -
307B ILE* 3.8 11.7 - - + -
308B SER* 3.2 19.5 + - - +
310B LYS* 1.3 76.2 - - - +
312B ARG* 1.3 64.8 + - - +
314B LEU* 3.4 5.0 + - - +
315B ILE* 3.1 28.2 + - - +
337B TRP* 3.4 29.7 - - + +
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Residues in contact with ARG 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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303B ILE* 2.7 57.0 + - + +
304B PRO 3.2 9.4 + - - -
305B GLU* 3.2 27.8 + - - +
307B ILE* 2.7 34.6 + - + +
308B SER 2.9 17.1 + - - +
309B PRO* 3.3 8.9 + - - +
311B ALA* 1.3 77.8 - - - +
313B CYS* 1.3 58.8 + - + +
314B LEU 3.3 0.2 - - - -
315B ILE* 3.4 5.6 + - - +
316B ARG* 3.1 31.0 + - - +
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Residues in contact with CYS 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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288A ASP* 2.8 44.9 - - + +
290A SER* 3.5 13.5 - - - -
309B PRO 3.2 15.9 + - - +
310B LYS* 3.8 11.0 - - - -
312B ARG* 1.3 77.5 - - + +
314B LEU* 1.3 54.1 + - - +
316B ARG* 4.1 11.2 - - + +
317B SER* 2.6 28.6 + - - -
335B HIS* 3.8 2.4 + - - -
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Residues in contact with LEU 314 (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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186B PHE* 4.5 2.5 - - + -
274B LEU* 3.4 25.4 - - + -
310B LYS 3.2 16.6 + - - +
311B ALA* 3.7 5.6 - - - +
312B ARG 3.3 0.2 - - - -
313B CYS* 1.3 77.2 - - - +
315B ILE* 1.3 63.9 + - - +
316B ARG 3.3 0.2 - - - -
317B SER* 3.3 4.3 + - - -
318B LEU* 3.2 34.5 + - + +
327B LEU* 4.2 10.8 - - + -
332B ILE* 4.2 15.7 - - + -
335B HIS* 3.7 32.3 - - + +
337B TRP* 3.5 33.2 - - + -
338B PHE* 4.2 14.6 - - + -
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Residues in contact with ILE 315 (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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271B GLY 4.9 2.5 - - - +
274B LEU* 3.7 21.3 - - + -
275B TYR* 4.0 29.4 - - + +
278B LEU* 4.2 17.5 - - + -
279B VAL* 5.6 0.7 - - + -
301B PHE* 4.0 6.7 - - + -
303B ILE* 3.6 33.7 - - + -
307B ILE* 4.5 4.0 - - + -
311B ALA 3.1 17.8 + - - +
312B ARG 3.4 6.3 + - - +
314B LEU* 1.3 77.9 - - - +
316B ARG* 1.3 57.9 + - - +
318B LEU* 3.0 7.3 + - - +
319B LEU* 2.9 50.4 + - + +
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Residues in contact with ARG 316 (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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301B PHE* 3.1 58.7 + - + -
302B CYS* 4.6 0.8 - - - +
303B ILE* 3.9 37.7 + - + +
312B ARG* 3.1 17.9 + - + +
313B CYS* 4.1 6.7 - - - -
315B ILE* 1.3 78.2 - - - +
317B SER* 1.3 59.9 + - - +
318B LEU 3.5 0.3 + - - -
319B LEU* 4.0 3.5 - - - +
320B ARG* 3.4 36.6 + - - +
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Residues in contact with SER 317 (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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286A ASP* 5.9 0.2 - - - -
288A ASP* 3.7 1.2 + - - +
291A ALA* 3.6 18.3 - - - +
313B CYS 2.6 23.8 + - - -
314B LEU* 3.3 11.8 + - - -
315B ILE 3.2 0.6 - - - -
316B ARG* 1.3 77.5 - - - +
318B LEU* 1.3 58.1 + - - +
320B ARG* 3.5 21.3 + - - +
325B GLU 4.4 0.5 - - - +
326B ARG* 3.4 24.6 - - - -
327B LEU* 3.5 30.2 + - - +
335B HIS* 4.5 0.7 + - - -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 4.2 16.8 - - + -
267B VAL* 3.8 18.8 - - + +
268B TRP* 4.0 7.8 - - - -
270B LEU 4.1 4.3 - - - -
271B GLY* 3.8 31.2 - - - +
274B LEU* 4.5 5.8 - - + -
314B LEU* 3.2 23.8 - - + +
315B ILE* 3.0 6.3 + - - +
317B SER* 1.3 74.7 - - - +
319B LEU* 1.3 61.3 + - - +
320B ARG 3.1 10.0 + - - -
326B ARG* 3.2 22.7 + - - -
327B LEU* 4.0 18.8 - - + -
332B ILE* 3.5 36.8 - - + -
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Residues in contact with LEU 319 (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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268B TRP* 3.4 57.3 - - + +
271B GLY* 3.7 13.9 - - - +
272B VAL* 3.6 13.0 - - + +
275B TYR* 4.7 1.3 - - + -
283B PRO* 4.3 19.5 - - + -
284B PHE* 5.1 2.5 - - + -
301B PHE* 3.7 44.5 - - + -
315B ILE* 2.9 29.2 + - + +
316B ARG* 4.0 6.6 - - - +
318B LEU* 1.3 75.9 - - - +
320B ARG* 1.3 59.8 + - - +
321B ARG* 3.9 2.8 + - - +
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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