Contacts of the helix formed by residues 314 - 327 (chain C) in PDB entry 3IO6
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 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C TRP* 5.2 0.5 - - - -
311C LEU 3.0 13.9 + - - +
312C ALA 4.2 0.4 - - - -
313C LYS* 1.3 75.7 - - - +
315C PRO* 1.4 76.5 - - - +
316C ARG* 3.3 47.1 + - - +
317C ILE* 3.1 33.7 + - + +
318C ALA* 3.2 10.7 + - - +
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Residues in contact with PRO 315 (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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244C VAL 4.4 8.2 - - - +
312C ALA 4.9 0.7 - - - +
313C LYS 3.2 10.9 - - - +
314C ASP* 1.4 89.7 - - - +
316C ARG* 1.3 57.3 + - + +
318C ALA* 3.1 10.2 + - + +
319C ALA* 2.7 37.4 + - - +
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Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TRP* 3.4 40.1 - - + +
236C ASP* 3.9 15.2 + - - -
242C TYR* 2.6 48.8 + - + +
243C GLY* 5.9 1.1 - - - -
244C VAL* 4.1 23.6 + - + +
314C ASP* 3.1 29.7 + - - +
315C PRO* 1.3 82.3 - - + +
317C ILE* 1.3 62.2 + - - +
319C ALA* 3.3 4.3 + - - +
320C THR* 3.2 22.2 + - - -
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Residues in contact with ILE 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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232C TRP* 4.4 10.3 - - + -
294C ASN* 6.1 2.0 - - - +
298C PRO* 6.2 4.0 - - + -
300C GLY* 4.1 26.0 - - - +
301C ALA* 4.1 22.3 - - + +
308C GLU* 5.2 4.3 - - + +
311C LEU* 4.3 35.7 - - + +
312C ALA* 4.7 1.8 - - + +
314C ASP* 3.1 31.8 + - + +
316C ARG* 1.3 74.8 - - - +
318C ALA* 1.3 63.8 + - - +
319C ALA 3.1 1.6 - - - -
320C THR* 2.9 23.9 + - - -
321C MET* 3.0 12.8 + - + +
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Residues in contact with ALA 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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312C ALA* 3.7 34.1 - - + +
314C ASP 3.2 3.9 + - - +
315C PRO* 3.1 11.8 + - + +
317C ILE* 1.3 79.0 - - - +
319C ALA* 1.3 56.7 + - - +
321C MET* 3.7 7.6 + - - +
322C GLU* 3.2 27.4 + - - +
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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
----------------------------------------------------------
114C SER* 4.3 1.1 - - - -
244C VAL* 3.5 28.9 - - + +
245C THR* 3.8 17.0 - - - -
246C VAL 4.5 0.2 - - - +
315C PRO 2.7 15.8 + - - +
316C ARG 3.5 6.5 - - - +
317C ILE 3.1 0.2 - - - -
318C ALA* 1.3 76.7 - - - +
320C THR* 1.3 62.2 + - - +
322C GLU* 3.9 9.9 - - - +
323C ASN* 2.8 33.4 + - - -
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Residues in contact with THR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL 4.1 16.2 - - - +
112C ALA* 3.7 31.1 - - - +
114C SER* 3.8 10.4 + - - -
229C PRO* 4.1 12.0 - - + +
232C TRP* 3.4 21.7 - - - -
300C GLY* 5.9 0.9 - - - -
301C ALA* 4.5 9.9 - - + +
316C ARG 3.2 13.6 + - - -
317C ILE* 2.9 10.0 + - - -
319C ALA* 1.3 76.4 - - - +
321C MET* 1.3 57.4 + - - +
323C ASN* 3.5 3.0 + - - +
324C ALA* 2.9 30.6 + - + +
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Residues in contact with MET 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.7 34.1 - - + +
92C PHE* 4.1 18.4 - - - -
110C VAL* 4.2 12.6 - - + -
301C ALA* 3.6 24.1 - - + +
302C VAL 3.5 25.1 - - - +
308C GLU* 4.3 9.2 - - + -
317C ILE* 3.0 14.1 + - + +
318C ALA* 4.0 8.1 - - - +
320C THR* 1.3 79.5 - - - +
322C GLU* 1.3 57.3 + - - +
324C ALA* 3.2 4.2 + - - +
325C GLN* 3.0 40.7 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C THR* 5.2 0.7 + - - -
246C VAL* 3.3 35.1 + - + +
318C ALA 3.2 16.7 + - - +
319C ALA* 4.0 6.9 - - - +
320C THR 3.3 0.2 - - - -
321C MET* 1.3 79.7 - - - +
323C ASN* 1.3 59.4 + - - +
325C GLN* 3.6 11.8 + - - +
326C LYS* 3.1 48.9 + - + +
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Residues in contact with ASN 323 (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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112C ALA* 4.2 4.7 - - + -
113C LEU 3.4 20.2 - - - +
114C SER* 3.5 15.1 - - - +
245C THR 3.4 22.4 + - - -
246C VAL* 3.6 9.0 - - - +
247C LEU* 2.9 35.7 + - - +
255C SER 5.5 0.7 - - - +
257C PRO* 3.6 14.3 - - + +
319C ALA 2.8 27.1 + - - +
320C THR 3.9 3.4 - - - +
322C GLU* 1.3 73.5 - - - +
324C ALA* 1.3 64.3 + - - +
326C LYS* 3.6 4.8 + - - +
327C GLY 3.3 17.3 + - - -
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Residues in contact with ALA 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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92C PHE* 3.8 13.4 - - + -
110C VAL* 3.3 34.3 - - + -
112C ALA* 3.7 15.0 - - + +
259C VAL* 3.5 23.0 - - + +
320C THR 2.9 18.9 + - - +
321C MET* 3.2 7.8 + - - +
323C ASN* 1.3 76.7 - - - +
325C GLN* 1.3 61.9 + - - +
326C LYS 3.5 0.2 - - - -
327C GLY 3.7 4.5 + - - +
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Residues in contact with GLN 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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90C TYR* 4.2 19.2 + - - -
92C PHE* 4.0 30.6 - - + +
321C MET* 3.0 35.0 + - - +
322C GLU* 4.0 12.7 - - - +
323C ASN 3.3 0.2 - - - -
324C ALA* 1.3 79.1 - - - +
326C LYS* 1.3 66.4 + - + +
327C GLY 3.9 4.9 - - - +
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Residues in contact with LYS 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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246C VAL* 3.8 20.2 - - - +
254C PRO* 4.0 39.3 - - + +
255C SER 4.4 6.3 - - - +
256C LYS* 3.3 28.9 + - - +
322C GLU* 3.1 45.1 + - + +
323C ASN* 3.6 4.0 + - - +
324C ALA 3.5 0.2 - - - -
325C GLN* 1.3 82.4 - - + +
327C GLY* 1.3 61.4 + - - +
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Residues in contact with GLY 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 6.1 0.3 - - - -
256C LYS* 3.9 4.4 + - - -
257C PRO* 3.4 27.8 - - - +
259C VAL* 4.2 4.7 - - - +
323C ASN 3.3 10.3 + - - -
324C ALA 3.7 6.3 + - - +
325C GLN 3.3 7.8 - - - +
326C LYS* 1.3 82.2 - - - +
328C GLU* 1.3 64.5 - - - +
329C ILE* 5.2 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