Contacts of the helix formed by residues 316 - 330 (chain A) in PDB entry 3C3C
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 GLY 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ASP* 3.0 30.1 + - - -
285A PHE* 4.1 6.7 - - - -
286A VAL* 5.0 2.7 - - - -
315A CYS* 1.3 76.2 - - - +
317A PRO* 1.3 64.0 - - - +
319A SER 3.2 1.6 + - - -
320A SER* 2.8 37.9 + - - -
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Residues in contact with PRO 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ASP* 3.6 7.6 - - - +
285A PHE 5.9 0.7 - - - +
286A VAL* 5.7 4.0 - - + -
316A GLY* 1.3 84.3 - - - +
318A GLU* 1.3 59.4 + - - +
320A SER* 3.3 10.3 - - - +
321A LYS* 3.1 27.9 + - - +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A VAL* 4.1 13.9 - - + -
284A ASP* 2.9 22.9 + - + +
317A PRO* 1.3 77.3 - - - +
319A SER* 1.3 55.8 + - - +
321A LYS* 3.3 41.6 + - - +
322A LYS* 3.1 29.8 + - + +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PRO* 3.3 9.3 - - - +
283A VAL* 2.7 34.7 + - - +
284A ASP* 2.7 25.3 + - - -
315A CYS* 3.6 20.2 - - - -
316A GLY 3.4 3.6 - - - -
318A GLU* 1.3 73.9 - - - +
320A SER* 1.3 65.4 + - - +
322A LYS* 3.2 6.9 + - - +
323A TYR* 3.0 31.8 + - - -
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A CYS* 4.1 9.9 - - - -
316A GLY 2.8 21.8 + - - -
317A PRO* 3.3 14.3 - - - +
319A SER* 1.3 73.2 - - - +
321A LYS* 1.3 60.6 + - - -
323A TYR* 3.5 12.2 + - - +
324A ALA* 3.2 22.6 + - - +
349A ARG 5.4 0.3 - - - -
350A GLY* 4.3 6.8 - - - -
353A ALA* 4.2 23.5 - - - +
354A LEU* 5.7 0.3 - - - +
357A GLU* 5.7 0.7 - - - +
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A PRO 3.1 13.2 + - - +
318A GLU* 3.4 42.9 + - - +
319A SER 3.2 0.6 - - - -
320A SER* 1.3 75.0 - - - +
322A LYS* 1.3 60.9 - - - +
324A ALA* 3.3 9.4 + - + +
325A GLU* 3.2 37.0 + - + +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LYS* 6.4 0.2 - - - +
279A ILE 5.3 1.2 + - - -
280A THR* 3.6 33.8 + - + +
281A LEU* 3.5 21.9 + - - +
283A VAL* 3.9 31.1 - - + +
318A GLU* 3.1 14.4 + - + +
319A SER* 3.5 9.4 - - - +
321A LYS* 1.3 72.9 - - - +
323A TYR* 1.3 67.6 + - + +
325A GLU* 3.3 24.0 + - - +
326A ALA* 3.6 8.3 + - - +
329A ARG* 5.3 0.7 + - - -
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Residues in contact with TYR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.5 41.5 - - + +
236A GLY* 4.0 11.1 - - - -
237A GLY 5.2 0.2 + - - -
280A THR* 3.9 20.0 - - + -
281A LEU 4.4 1.1 - - - -
282A PRO* 3.4 40.2 - - + +
315A CYS* 3.8 25.0 - - - +
319A SER* 3.0 21.2 + - - -
320A SER* 3.7 9.2 - - - +
322A LYS* 1.3 74.7 - - + +
324A ALA* 1.3 60.8 + - - +
326A ALA* 3.1 7.1 + - - +
327A VAL* 3.0 26.2 + - - +
339A VAL* 4.1 18.1 - - + +
350A GLY 5.4 1.6 - - - -
354A LEU* 4.0 30.7 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A SER 3.2 11.7 + - - +
321A LYS* 3.4 13.9 - - + +
322A LYS 3.2 0.2 - - - -
323A TYR* 1.3 77.5 - - - +
325A GLU* 1.3 58.4 + - + +
327A VAL* 3.2 11.6 + - - +
328A THR* 2.8 33.7 + - - +
354A LEU* 5.1 0.6 - - - +
357A GLU* 3.7 33.5 - - + +
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LYS* 3.2 26.6 + - + +
322A LYS* 3.6 17.7 - - - +
323A TYR 3.2 0.6 - - - -
324A ALA* 1.3 77.2 - - + +
326A ALA* 1.3 62.5 + - - +
328A THR* 3.6 8.3 + - - -
329A ARG* 3.3 45.3 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.0 24.2 - - + +
232A GLU* 3.5 21.4 - - - +
234A ILE* 4.3 10.5 - - + -
280A THR* 4.7 5.2 - - - +
322A LYS 3.6 5.6 + - - +
323A TYR 3.1 9.4 + - - +
325A GLU* 1.3 75.6 - - - +
327A VAL* 1.3 67.6 + - - +
329A ARG* 3.2 23.7 + - - +
330A ALA* 3.2 14.9 + - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.1 18.6 - - + -
210A ILE* 4.6 2.9 - - + -
234A ILE* 4.9 0.9 - - + -
323A TYR 3.0 19.5 + - - +
324A ALA* 3.2 11.6 + - - +
326A ALA* 1.3 76.1 - - - +
328A THR* 1.3 61.4 + - - +
330A ALA* 3.2 19.9 + - - +
333A ILE* 4.1 9.5 - - + +
354A LEU* 3.9 24.5 - - + -
357A GLU* 3.3 37.2 - - + +
358A VAL* 4.0 9.2 - - + +
361A ALA* 4.0 13.8 - - + +
364A ARG* 4.2 6.5 + - - +
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ALA* 2.8 23.3 + - - +
325A GLU* 3.7 10.2 - - - -
327A VAL* 1.3 74.3 - - - +
329A ARG* 1.3 62.6 + - + +
330A ALA 3.6 3.8 + - - +
357A GLU* 5.4 2.6 + - - -
364A ARG* 3.9 23.3 + - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO* 3.2 29.4 - - + +
232A GLU* 2.8 46.1 + - - +
278A LYS* 3.6 24.7 - - - +
280A THR* 5.0 1.4 + - - -
322A LYS 5.3 1.0 + - - -
325A GLU* 3.3 31.2 + - - +
326A ALA* 3.2 18.7 + - - +
328A THR* 1.3 80.1 - - + +
330A ALA* 1.3 61.3 + - - +
331A LYS* 4.8 1.0 - - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO* 3.5 9.2 - - - +
208A LEU* 3.9 10.8 - - + -
232A GLU* 5.5 0.2 + - - -
326A ALA 3.2 10.4 + - - +
327A VAL 3.2 16.4 + - - +
328A THR 4.3 3.1 - - - +
329A ARG* 1.3 78.0 - - - +
331A LYS* 1.3 63.9 + - - +
332A GLN 3.9 7.4 - - - +
333A ILE* 3.8 27.6 - - + -
361A ALA* 5.6 0.3 - - - +
364A ARG* 5.9 0.5 + - - -
366A CYS* 3.4 12.5 - - - +
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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