Contacts of the helix formed by residues 315 - 328 (chain A) in PDB entry 3Q29
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 ASP 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A TRP* 4.4 1.2 - - - -
311A GLU 3.7 7.3 + - - +
312A LEU* 3.3 8.3 + - + +
313A ALA 3.3 3.6 - - - +
314A LYS* 1.3 75.8 - - - +
316A PRO* 1.3 65.1 - - - +
317A ARG* 2.7 57.6 + - - +
318A ILE* 3.0 40.7 + - + +
319A ALA* 3.2 8.7 + - - +
180C LYS* 5.1 0.2 + - - -
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Residues in contact with PRO 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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245A VAL 4.6 2.5 - - - +
314A LYS 3.0 11.8 - - - +
315A ASP* 1.3 85.8 - - - +
317A ARG* 1.3 63.3 + - + +
318A ILE 3.3 0.2 - - - -
319A ALA* 3.2 13.2 + - + +
320A ALA* 2.9 27.2 + - - +
180C LYS* 5.7 1.1 - - - +
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Residues in contact with ARG 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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233A TRP* 3.4 51.2 - - + +
237A ASP* 3.8 13.9 + - - -
243A TYR* 3.0 31.5 + - + -
244A GLY* 6.3 0.2 - - - -
245A VAL* 3.6 27.8 - - + +
295A ASN* 6.2 0.2 - - - +
299A PRO* 4.7 8.7 - - - +
315A ASP* 2.7 32.6 + - - +
316A PRO* 1.3 79.8 - - + +
318A ILE* 1.3 58.9 - - - +
320A ALA* 3.3 4.3 + - - +
321A THR* 2.8 30.1 + - - -
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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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233A TRP* 4.0 15.0 - - + -
295A ASN* 5.9 0.7 - - - +
299A PRO* 5.8 1.3 - - + -
301A GLY* 3.3 38.1 - - - +
302A ALA* 4.3 19.5 - - + +
312A LEU* 3.8 35.2 - - + +
315A ASP* 3.0 31.7 + - + +
317A ARG* 1.3 77.3 - - - +
319A ALA* 1.3 56.4 + - - +
321A THR* 3.3 6.4 + - - +
322A MET* 2.8 28.7 + - + +
372C MET* 4.4 8.3 - - + -
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Residues in contact with ALA 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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312A LEU 5.3 0.2 + - - -
315A ASP 3.2 2.8 + - - +
316A PRO* 3.2 20.6 + - + +
317A ARG 3.1 0.4 - - - -
318A ILE* 1.3 77.1 - - - +
320A ALA* 1.3 60.4 + - - +
322A MET* 3.3 7.9 + - - +
323A GLU* 2.8 32.6 + - - +
180C LYS* 3.9 31.0 - - - +
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Residues in contact with ALA 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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115A SER* 3.7 2.9 - - - +
245A VAL* 3.3 39.7 - - + +
246A THR* 3.8 13.0 - - - +
316A PRO 2.9 10.1 + - - +
317A ARG 3.5 7.6 - - - +
319A ALA* 1.3 75.3 - - - +
321A THR* 1.3 58.3 + - - +
323A GLU* 3.2 13.1 + - - +
324A ASN* 2.8 34.1 + - - -
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Residues in contact with THR 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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111A VAL* 4.5 10.5 - - + +
112A GLU 4.7 0.2 - - - -
113A ALA* 3.8 32.4 + - + +
115A SER* 3.5 12.8 + - - -
230A PRO* 4.2 11.8 - - + +
233A TRP* 3.4 21.7 - - - -
301A GLY* 5.0 3.8 - - - -
302A ALA 5.1 1.8 - - - +
317A ARG 2.8 18.7 + - - -
318A ILE* 3.3 12.6 - - - -
320A ALA* 1.3 74.8 - - - +
322A MET* 1.3 62.7 + - + +
324A ASN* 3.2 4.6 + - - +
325A ALA* 2.8 27.6 + - + +
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Residues in contact with MET 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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111A VAL* 3.9 26.5 - - + +
302A ALA* 3.3 26.9 - - + -
318A ILE* 2.8 22.3 + - + +
319A ALA* 3.5 7.4 - - - +
321A THR* 1.3 75.1 - - + +
323A GLU* 1.3 63.6 + - - +
325A ALA* 3.1 7.0 + - + +
326A GLN* 2.9 31.2 + - + +
179C ILE* 6.2 4.5 - - + -
372C MET* 4.2 25.1 - - + +
375C PHE* 4.1 25.8 - - + -
376C MET* 5.1 3.4 - - + -
379C LEU* 4.4 17.7 - - + -
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Residues in contact with GLU 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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247A VAL* 3.8 31.4 + - + +
319A ALA* 2.8 14.8 + - - +
320A ALA* 3.2 15.8 + - - +
322A MET* 1.3 77.5 - - - +
324A ASN* 1.3 61.8 + - - +
326A GLN* 3.3 17.6 + - - +
327A LYS* 3.4 24.2 + - + +
176C LYS* 3.6 32.9 - - - +
179C ILE* 6.0 13.2 - - + +
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Residues in contact with ASN 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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113A ALA* 4.6 0.7 - - + -
114A LEU 3.3 20.2 - - - +
115A SER* 2.8 37.5 + - - +
246A THR 3.2 11.9 + - - -
247A VAL* 3.5 9.5 - - - +
248A LEU* 2.9 31.8 + - - +
256A SER 5.4 1.0 - - - +
258A PRO* 3.5 18.7 - - + +
320A ALA 2.8 20.4 + - - +
321A THR 3.6 4.0 - - - +
323A GLU* 1.3 73.7 - - - +
325A ALA* 1.3 63.7 + - - +
327A LYS* 3.3 7.1 + - - +
328A GLY 3.0 16.8 + - - -
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Residues in contact with ALA 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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111A VAL* 4.7 1.3 - - + -
113A ALA* 3.9 15.9 - - + +
258A PRO* 5.1 0.2 - - - -
260A VAL* 3.5 32.7 - - + +
321A THR* 2.8 17.4 + - + +
322A MET* 3.1 19.5 + - + +
324A ASN* 1.3 76.6 - - - +
326A GLN* 1.3 62.8 + - - +
328A GLY* 3.2 11.1 + - - +
379C LEU* 3.7 19.3 - - + +
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Residues in contact with GLN 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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322A MET* 2.9 25.5 + - + +
323A GLU* 3.6 8.5 - - - +
324A ASN 3.3 0.2 - - - -
325A ALA* 1.3 76.3 - - - +
327A LYS* 1.3 65.2 + - + +
328A GLY 3.4 5.4 + - - +
73C GLN* 3.2 29.9 + - - +
179C ILE* 4.5 15.2 - - + +
335C PRO* 6.2 1.2 - - - +
336C GLN* 4.8 16.4 + - - +
375C PHE* 3.6 29.6 - - - +
378C GLY* 4.0 21.0 + - - -
379C LEU* 3.8 21.8 - - + +
382C ALA* 5.0 7.1 - - - +
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Residues in contact with LYS 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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247A VAL* 4.6 21.3 - - + -
255A PRO* 3.3 34.6 - - + +
256A SER 4.1 5.4 - - - +
257A LYS* 3.4 27.0 - - - +
323A GLU* 3.6 19.3 - - - +
324A ASN* 3.3 10.7 + - - +
326A GLN* 1.3 79.9 - - + +
328A GLY* 1.3 59.4 + - - +
73C GLN* 4.8 7.1 - - - +
100C TYR* 4.9 6.3 + - - -
101C ASN* 3.0 31.7 + - - +
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Residues in contact with GLY 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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257A LYS* 3.8 7.0 - - - -
258A PRO* 3.1 23.1 - - - -
260A VAL* 4.4 0.9 - - - -
324A ASN 3.0 11.9 + - - -
325A ALA 3.2 11.7 + - - +
326A GLN 3.8 6.4 - - - +
327A LYS* 1.3 82.9 - - - +
329A GLU* 1.3 67.5 + - - +
382C ALA* 5.9 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