Contacts of the helix formed by residues 315 - 328 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C TRP* 4.2 2.8 - - - -
295C ASN* 5.6 3.1 + - - -
299C PRO* 5.8 0.3 - - - +
311C GLU 5.0 1.3 - - - +
312C LEU* 2.9 20.1 + - + +
313C ALA 3.2 3.0 - - - -
314C LYS* 1.3 79.0 - - - +
316C PRO* 1.3 66.4 - - - +
317C ARG* 2.7 56.9 + - - +
318C ILE* 3.0 35.2 + - + +
319C ALA* 3.6 3.1 + - - +
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Residues in contact with PRO 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL 5.0 0.9 - - - +
314C LYS 3.3 11.9 - - - +
315C ASP* 1.3 85.4 - - - +
317C ARG* 1.3 63.3 + - + +
318C ILE 3.2 0.2 - - - -
319C ALA* 3.1 25.9 + - + +
320C ALA* 3.2 7.8 + - - +
396C GOL 4.7 25.3 - - - +
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Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TRP* 3.4 53.9 - - + +
237C ASP* 3.9 14.3 + - - -
243C TYR* 3.0 34.9 + - + -
245C VAL* 3.7 22.0 - - + -
295C ASN* 5.7 2.6 - - - +
299C PRO* 4.4 10.1 - - - +
315C ASP* 2.7 31.5 + - - +
316C PRO* 1.3 80.0 - - + +
318C ILE* 1.3 55.3 + - - +
320C ALA* 3.2 5.9 + - - +
321C THR* 3.0 27.5 + - - -
396C GOL 4.2 11.7 - - - +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C TRP* 3.8 19.5 - - + -
295C ASN* 6.1 0.4 - - - +
299C PRO* 6.0 0.7 - - + -
301C GLY* 3.6 35.7 - - - +
302C ALA* 4.5 13.5 - - + -
312C LEU* 4.3 31.4 - - + +
315C ASP* 3.0 30.6 + - + +
317C ARG* 1.3 73.6 - - - +
319C ALA* 1.3 60.2 + - - +
321C THR* 3.1 6.3 + - - +
322C MET* 2.8 50.5 + - + +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP 3.6 3.2 + - - +
316C PRO* 3.1 18.5 + - + +
318C ILE* 1.3 79.1 - - - +
320C ALA* 1.3 57.3 + - - +
322C MET* 3.2 17.7 + - + +
323C GLU* 3.0 29.8 + - - +
397C GOL 5.1 0.9 + - - -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.8 2.0 - - - -
245C VAL* 3.1 43.1 - - + +
246C THR* 3.8 11.2 - - - +
247C VAL 4.7 0.2 - - - +
316C PRO 3.2 6.3 + - - +
317C ARG 3.2 9.4 + - - +
319C ALA* 1.3 76.2 - - - +
321C THR* 1.3 64.6 + - - +
323C GLU* 3.3 10.7 + - - +
324C ASN* 3.1 30.0 + - - -
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Residues in contact with THR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 4.4 11.9 - - + +
112C GLU 4.8 0.2 - - - -
113C ALA* 3.9 32.5 + - + +
115C SER* 3.8 11.1 + - - -
230C PRO* 4.1 11.6 - - + +
233C TRP* 3.5 22.9 - - - -
301C GLY* 5.0 4.0 - - - -
302C ALA* 5.0 3.6 - - + +
317C ARG 3.0 14.5 + - - -
318C ILE* 3.1 14.6 + - + -
320C ALA* 1.3 75.8 - - - +
322C MET* 1.3 60.3 + - + +
324C ASN* 3.4 1.1 + - - -
325C ALA* 2.9 28.4 + - + +
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Residues in contact with MET 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ALA* 4.6 16.4 - - + -
318C ILE* 2.8 40.3 + - + +
319C ALA* 3.6 17.7 - - + +
321C THR* 1.3 74.6 - - + +
323C GLU* 1.3 57.8 + - - +
325C ALA* 3.2 7.6 + - - +
326C GLN* 2.9 34.0 + - + +
397C GOL 4.0 35.9 - - - +
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C VAL* 3.7 34.4 + - + +
319C ALA 3.0 16.8 + - - +
320C ALA* 3.7 10.5 - - - +
322C MET* 1.3 78.1 - - - +
324C ASN* 1.3 61.3 + - - +
326C GLN* 3.6 7.8 + - - +
327C LYS* 3.4 41.4 + - - +
397C GOL 4.3 11.8 + - - +
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ALA* 4.4 0.7 - - + -
114C LEU 3.2 20.4 - - - +
115C SER* 3.0 27.0 + - - +
246C THR 3.1 20.8 + - - -
247C VAL* 3.6 11.3 - - - +
248C LEU* 2.8 33.5 + - - +
256C SER 5.2 1.7 - - - +
258C PRO* 3.2 21.5 - - + +
320C ALA 3.1 17.2 + - - +
321C THR 3.9 2.9 - - - +
323C GLU* 1.3 73.7 - - - +
325C ALA* 1.3 66.0 + - - +
327C LYS* 3.3 5.7 + - - +
328C GLY 3.2 16.3 + - - -
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 4.7 10.3 - - + -
113C ALA* 3.8 14.7 - - + +
260C VAL* 3.5 34.8 - - + +
321C THR* 2.9 19.8 + - + +
322C MET* 3.5 8.1 - - - +
324C ASN* 1.3 74.7 - - - +
326C GLN* 1.3 65.4 + - - +
328C GLY* 2.9 14.7 + - - +
330C ILE* 5.6 0.9 - - - +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C MET* 2.9 16.8 + - + +
323C GLU* 3.8 10.0 - - - +
324C ASN 3.4 0.2 - - - -
325C ALA* 1.3 76.7 - - + +
327C LYS* 1.3 62.2 + - + +
328C GLY 3.6 4.5 + - - +
397C GOL 2.8 50.0 + - - -
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Residues in contact with LYS 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C VAL* 3.5 31.3 - - + +
255C PRO* 3.7 33.2 - - + +
256C SER 3.9 14.4 - - - +
257C LYS* 3.1 27.7 - - - +
323C GLU* 3.4 32.4 + - - +
324C ASN* 3.3 7.1 + - - +
325C ALA 3.1 1.2 - - - -
326C GLN* 1.3 79.4 - - + +
328C GLY* 1.3 60.4 + - - +
329C GLU* 5.1 0.5 - - - +
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Residues in contact with GLY 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 3.9 3.4 - - - -
258C PRO* 3.1 28.7 - - - -
260C VAL* 4.4 1.1 - - - +
324C ASN 3.2 4.8 + - - -
325C ALA 2.9 16.1 + - - +
326C GLN 4.0 4.3 - - - +
327C LYS* 1.3 82.7 - - - +
329C GLU* 1.3 72.9 + - - +
330C ILE* 5.6 1.2 - - - +
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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