Contacts of the helix formed by residues 308 - 321 (chain A) in PDB entry 3ECP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU* 4.2 3.1 - - - -
306A VAL 3.3 5.6 - - - +
307A GLU* 1.3 77.0 - - - +
309A LEU* 1.3 66.3 + - - +
310A ALA* 3.5 7.2 + - - +
311A GLN* 2.8 43.5 + - - +
312A ALA* 3.1 16.6 + - - +
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Residues in contact with LEU 309 (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 LEU* 3.4 38.6 - - + +
235A GLY* 3.9 22.0 - - - -
236A GLY 4.5 7.6 - - - +
265A LEU* 4.0 21.3 - - + -
308A SER* 1.3 72.3 - - - +
310A ALA* 1.3 58.5 + - - +
312A ALA* 3.1 5.2 + - - +
313A LEU* 2.9 38.2 + - + +
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Residues in contact with ALA 310 (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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308A SER* 3.3 7.7 + - - +
309A LEU* 1.3 79.2 - - - +
311A GLN* 1.3 57.5 + - - +
313A LEU* 3.1 8.9 + - - +
314A ARG* 2.9 29.0 + - - +
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Residues in contact with GLN 311 (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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305A PRO* 3.6 42.5 - - + +
306A VAL* 3.9 2.9 - - - -
307A GLU* 3.3 14.8 + - - +
308A SER* 2.8 43.5 + - - +
310A ALA* 1.3 75.3 - - - +
312A ALA* 1.3 60.8 + - - +
314A ARG* 3.3 19.9 - - - +
315A VAL* 3.3 14.6 + - - +
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Residues in contact with ALA 312 (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 LEU* 3.8 17.9 - - + -
265A LEU* 3.8 16.8 - - + -
267A SER* 4.9 0.2 - - - -
282A VAL* 4.1 18.6 - - + +
306A VAL* 3.9 7.3 + - - +
308A SER 3.1 12.1 + - - +
309A LEU 3.4 9.0 - - - +
311A GLN* 1.3 76.0 - - - +
313A LEU* 1.3 64.0 + - - +
315A VAL* 3.2 10.1 + - - +
316A ILE* 3.1 24.9 + - - +
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Residues in contact with LEU 313 (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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236A GLY 4.9 2.5 - - - +
237A TYR* 3.5 37.9 - - + -
265A LEU* 3.3 26.9 - - + -
309A LEU* 2.9 27.6 + - + +
310A ALA* 3.1 9.6 + - - +
312A ALA* 1.3 73.9 - - - +
314A ARG* 1.3 67.0 + - - +
316A ILE* 3.0 9.6 + - + +
317A ASP* 2.8 32.1 + - - +
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Residues in contact with ARG 314 (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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91A GLU* 2.8 32.2 + - - +
134A ALA* 2.9 33.1 + - - +
135A THR* 4.8 2.0 + - - +
137A PHE* 4.1 18.0 - - - -
304A GLU* 6.3 2.0 - - + -
310A ALA 2.9 11.5 + - - +
311A GLN* 3.3 15.9 - - - +
313A LEU* 1.3 73.9 - - - +
315A VAL* 1.3 58.0 + - + +
317A ASP* 3.9 6.1 - - - +
318A ILE* 3.0 59.9 + - + +
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Residues in contact with VAL 315 (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 VAL* 4.1 17.3 - - + +
282A VAL* 3.9 18.6 - - + -
300A LEU* 3.9 20.6 - - + -
302A THR* 4.2 8.7 - - + +
304A GLU* 4.2 18.2 - - + -
305A PRO 4.0 13.0 - - - +
306A VAL* 4.1 12.3 - - + -
311A GLN 3.3 14.8 + - - +
312A ALA 3.2 8.6 + - - +
313A LEU 3.0 1.0 - - - -
314A ARG* 1.3 76.7 - - + +
316A ILE* 1.3 67.4 + - - +
318A ILE* 3.2 9.6 + - + +
319A TYR* 3.1 20.1 + - - +
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Residues in contact with ILE 316 (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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237A TYR* 3.3 37.9 - - + +
265A LEU* 3.9 22.9 - - + -
282A VAL* 4.3 9.6 - - + -
284A ALA* 4.1 10.1 - - + +
298A TRP* 4.0 9.7 - - + -
300A LEU* 3.9 23.1 - - + -
312A ALA 3.1 12.9 + - - +
313A LEU* 3.0 12.7 + - + +
315A VAL* 1.3 75.0 - - - +
317A ASP* 1.3 69.5 + - - +
319A TYR* 3.1 7.1 + - - +
320A THR* 2.9 30.9 + - - +
2C T 3.6 10.5 - - + +
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Residues in contact with ASP 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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137A PHE* 5.5 5.5 - - + -
237A TYR* 5.8 1.9 - - - -
313A LEU* 2.8 20.2 + - - +
314A ARG* 4.4 6.7 - - - +
316A ILE* 1.3 85.2 - - - +
318A ILE* 1.3 60.5 + - - +
320A THR* 3.1 20.0 + - - +
321A HIS* 2.6 44.3 + - - +
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Residues in contact with ILE 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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93A LEU* 4.2 22.5 - - + +
95A ILE* 5.7 0.3 - - - +
137A PHE* 5.5 1.3 - - + -
184A ILE* 3.7 31.9 - - + -
186A VAL* 3.6 32.6 - - + +
208A VAL* 4.0 17.7 - - + -
304A GLU* 4.8 9.0 - - + -
314A ARG* 3.0 57.5 + - + +
315A VAL* 3.5 8.3 - - + +
317A ASP* 1.3 77.0 - - - +
319A TYR* 1.3 61.8 + - - +
321A HIS* 3.5 16.6 + - - +
322A ARG 4.4 0.3 + - - -
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Residues in contact with TYR 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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186A VAL* 3.8 15.7 - - + -
187A CYS 3.5 21.3 - - - -
188A ASP* 3.3 19.8 - - - -
208A VAL* 4.2 11.7 - - + -
210A ARG* 3.3 26.6 - - + +
298A TRP* 3.5 33.7 - + + -
300A LEU* 3.8 22.9 - - + -
315A VAL 3.1 4.6 + - - +
316A ILE 3.1 9.9 + - - +
318A ILE* 1.3 75.7 - - - +
320A THR* 1.3 56.6 + - - +
321A HIS 2.9 5.6 - - - -
322A ARG* 2.9 37.0 + - - +
1C C 2.9 40.1 + - - -
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Residues in contact with THR 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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298A TRP* 3.6 22.4 - - - -
316A ILE* 2.9 18.4 + - - +
317A ASP* 3.1 23.9 + - - +
319A TYR* 1.3 74.2 - - - +
321A HIS* 1.3 61.7 + - + +
322A ARG 3.4 0.4 + - - -
323A TRP* 3.1 20.4 + - - +
2C T 3.8 20.6 + - + +
3C G 6.0 0.2 - - - +
4C A 5.4 2.8 + - - +
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Residues in contact with HIS 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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93A LEU* 4.6 6.7 - - + -
95A ILE* 3.2 21.4 - - + +
132A LEU* 4.8 2.2 - - + +
137A PHE* 3.2 63.2 - + + +
317A ASP* 2.6 38.9 + - - -
318A ILE* 3.8 9.9 - - - +
319A TYR 2.9 1.0 + - - -
320A THR* 1.3 82.1 - - + +
322A ARG* 1.3 62.8 + - - +
323A TRP* 3.3 16.8 + - - +
324A ARG* 3.1 23.7 + - + +
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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