Contacts of the helix formed by residues 304 - 313 (chain C) in PDB entry 6XWQ
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 PHE 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C SER 5.8 0.2 - - - -
68C LEU* 3.9 20.9 - - + -
71C GLY* 4.1 5.4 - - - +
72C ALA* 4.5 11.9 - - + -
75C ILE* 3.8 20.9 - - + -
80C LEU* 3.6 26.0 - - + -
83C VAL* 4.2 17.5 - - + -
84C GLY* 4.1 23.6 - - - -
87C ILE* 4.7 3.4 - - + -
161C ILE* 3.5 34.8 - - + -
299C LYS 4.5 0.4 + - - -
300C GLY 4.3 3.1 - - - +
301C ILE 3.4 1.8 + - - -
302C PHE 3.5 0.2 - - - -
303C SER* 1.3 79.4 - - - +
305C THR* 1.3 68.0 + - + +
306C LEU 3.4 1.1 - - - -
307C PRO* 3.3 4.9 - - - +
308C LEU* 3.0 39.4 + - + +
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Residues in contact with THR 305 (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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83C VAL* 3.6 30.5 - - + -
87C ILE* 3.9 27.1 - - + -
91C TYR* 3.1 9.9 + - - -
301C ILE* 2.5 33.8 + - + +
302C PHE* 4.1 0.2 - - - -
304C PHE* 1.3 76.2 - - + +
306C LEU* 1.3 55.5 + - - +
308C LEU* 3.0 5.5 + - - +
309C GLY 2.4 35.5 + - - -
413C THR* 2.7 25.6 + - - +
416C VAL* 4.8 2.0 - - + -
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 5.6 0.7 - - - +
284C LEU* 3.6 7.0 - - + +
287C THR* 3.9 15.0 - - + +
288C MET* 4.3 13.0 - - + -
291C ALA* 3.6 30.7 - - + -
301C ILE 4.1 0.6 + - - -
302C PHE* 3.8 15.5 - - + +
305C THR* 1.3 82.2 + - - +
307C PRO* 1.3 68.4 - - + +
309C GLY 4.3 0.4 - - - +
310C ALA* 3.1 29.1 + - + +
409C ASP* 3.6 41.7 - - + +
410C LEU* 3.8 14.6 - - + -
413C THR* 3.6 17.7 - - + +
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Residues in contact with PRO 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 4.8 0.9 - - - +
67C SER* 3.0 28.5 - - - +
68C LEU* 3.5 20.5 - - + +
197C TYR* 4.5 0.9 - - - +
284C LEU* 4.4 16.0 - - + +
288C MET* 4.4 13.5 - - + -
302C PHE 3.6 12.1 - - - +
303C SER* 3.2 22.0 - - - +
304C PHE* 3.3 14.4 - - - +
306C LEU* 1.3 93.7 - - + +
308C LEU* 1.3 58.3 + - - +
310C ALA* 4.2 1.2 + - - +
311C THR* 3.4 18.4 + - - -
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.1 15.2 - - + +
87C ILE* 4.5 17.5 - - + -
88C VAL* 4.9 8.1 - - + -
91C TYR* 4.4 3.6 - - + -
157C ILE* 3.9 32.5 - - + -
161C ILE* 5.2 3.8 - - + -
304C PHE* 3.0 42.8 + - + +
305C THR* 3.4 3.6 - - - +
307C PRO* 1.3 77.2 - - - +
309C GLY* 1.3 66.1 + - - +
311C THR* 2.9 15.5 + - - -
312C ILE* 3.2 42.1 + - + +
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Residues in contact with GLY 309 (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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91C TYR* 3.1 30.4 + - - -
305C THR 2.4 22.0 + - - -
306C LEU* 4.2 0.7 - - - -
308C LEU* 1.3 67.7 - - - +
310C ALA* 1.3 55.6 + - - +
311C THR 3.0 2.0 + - - -
313C ASN* 2.9 25.7 + - - +
409C ASP* 2.8 24.7 - - - +
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Residues in contact with ALA 310 (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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280C SER* 2.4 39.1 + - - +
281C SER* 4.0 8.1 + - - -
283C THR* 6.3 0.2 - - + -
284C LEU* 3.6 23.8 - - + -
287C THR* 5.6 2.7 - - + -
306C LEU* 3.1 21.1 + - + +
307C PRO 4.7 0.7 - - - +
308C LEU 3.1 0.4 + - - -
309C GLY* 1.3 74.0 - - - +
311C THR* 1.3 63.1 + - - +
313C ASN 5.0 0.4 - - - -
314C MET* 4.5 3.0 - - - +
357C GLY* 4.8 0.5 - - - -
406C VAL* 5.9 2.7 - - + -
409C ASP* 3.1 15.8 + - + +
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Residues in contact with THR 311 (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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60C VAL* 5.7 4.0 - - + +
64C VAL* 3.8 17.1 - - + +
153C VAL* 3.5 32.0 - - + +
157C ILE* 3.6 15.0 - - + -
281C SER* 4.9 7.3 + - - -
284C LEU* 5.4 3.1 - - - +
307C PRO 3.4 13.6 + - - -
308C LEU 2.9 7.5 + - - -
309C GLY 3.0 0.4 + - - -
310C ALA* 1.3 83.1 + - - +
312C ILE* 1.3 60.9 + - - +
314C MET* 3.4 11.8 - - - +
353C ILE 3.4 5.4 - - - +
355C THR 3.2 22.4 - - - +
357C GLY 5.2 7.0 - - - +
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Residues in contact with ILE 312 (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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88C VAL* 5.4 6.5 - - + -
91C TYR* 3.9 22.2 - - + -
92C LEU* 6.4 1.3 - - + -
95C SER* 5.4 0.3 + - - -
153C VAL* 5.6 0.4 - - + -
154C LEU* 3.7 21.3 - - + -
157C ILE* 3.6 25.8 - - + -
308C LEU* 3.2 36.3 + - + +
311C THR* 1.3 84.0 - - + +
313C ASN* 1.3 62.1 + - - +
314C MET* 2.9 13.6 + - - +
352C SER* 5.1 0.2 + - - -
353C ILE* 3.5 48.5 + - + +
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Residues in contact with ASN 313 (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* 4.6 0.8 - - - -
91C TYR* 3.4 44.7 - - + -
94C THR* 3.9 5.4 + - - -
95C SER* 4.4 5.5 + - - -
280C SER* 5.7 0.3 + - - -
309C GLY* 2.9 22.4 + - - +
312C ILE* 1.3 76.7 - - - +
314C MET* 1.3 63.1 + - - +
315C ASP* 3.5 23.1 + - - +
405C ASN* 4.3 8.2 + - - +
408C GLY* 3.6 6.3 + - - -
409C ASP* 2.3 52.7 + - - +
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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