Contacts of the helix formed by residues 304 - 313 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER 5.7 0.2 - - - -
68B LEU* 3.8 20.9 - - + -
71B GLY* 3.9 7.6 - - - +
72B ALA* 4.3 12.6 - - + -
75B ILE* 3.8 21.5 - - + -
80B LEU* 3.6 25.1 - - + -
83B VAL* 3.9 24.5 - - + -
84B GLY* 4.3 14.6 - - - -
87B ILE* 4.6 6.1 - - + -
161B ILE* 3.5 34.8 - - + -
299B LYS 5.1 0.2 + - - -
300B GLY 4.9 0.4 + - - +
301B ILE 2.9 5.4 + - - +
303B SER* 1.3 79.8 - - - +
305B THR* 1.3 66.8 + - + +
306B LEU 3.3 0.9 - - - -
307B PRO* 3.3 5.6 - - - +
308B LEU* 3.1 37.1 + - + +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.7 30.5 - - + -
87B ILE* 3.8 31.9 - - + -
91B TYR* 2.9 11.3 + - - -
301B ILE* 2.7 36.9 + - + +
304B PHE* 1.3 75.5 - - + +
306B LEU* 1.3 52.7 + - - +
308B LEU* 3.3 4.0 + - - +
309B GLY 2.6 32.1 + - - -
413B THR* 3.1 23.3 + - - -
416B VAL* 4.5 1.8 - - + -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 5.6 0.4 - - - +
284B LEU* 4.4 5.6 - - + -
287B THR* 3.9 23.1 - - + +
288B MET* 4.2 11.4 - - + -
291B ALA* 3.7 29.8 - - + -
301B ILE 4.1 0.6 + - - -
302B PHE* 3.8 19.1 - - + +
305B THR* 1.3 81.0 + - - +
307B PRO* 1.3 67.5 - - + +
309B GLY 4.2 0.2 - - - +
310B ALA* 2.9 35.1 + - + +
409B ASP* 3.7 29.6 - - + +
410B LEU* 4.0 7.6 - - + -
413B THR* 3.6 28.7 - - + +
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Residues in contact with PRO 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.7 1.0 - - - +
67B SER* 3.0 30.5 - - - +
68B LEU* 3.5 23.9 - - + +
197B TYR* 4.4 8.1 - - - +
284B LEU* 4.4 16.7 - - + +
288B MET* 4.5 7.0 - - - -
302B PHE 3.9 2.5 - - - +
303B SER* 3.2 26.2 - - - +
304B PHE* 3.3 14.4 - - - +
306B LEU* 1.3 93.7 - - + +
308B LEU* 1.3 55.0 + - - +
310B ALA* 4.6 0.7 - - - +
311B THR* 3.2 22.3 + - - -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.2 13.4 - - + +
87B ILE* 4.6 11.4 - - + -
88B VAL* 4.7 8.7 - - + -
91B TYR* 4.3 8.5 - - + -
157B ILE* 3.8 31.6 - - + -
161B ILE* 5.2 4.3 - - + -
304B PHE* 3.1 41.4 + - + +
305B THR 3.7 2.7 - - - +
306B LEU 3.1 0.6 - - - -
307B PRO* 1.3 76.6 - - - +
309B GLY* 1.3 66.0 + - - +
310B ALA 3.2 0.2 - - - -
311B THR* 3.0 5.1 + - - -
312B ILE* 2.9 57.6 + - + +
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Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 3.1 32.1 + - - -
305B THR 2.6 16.8 + - - -
306B LEU* 3.9 0.9 - - - -
308B LEU* 1.3 73.0 - - - +
310B ALA* 1.3 58.3 + - - +
311B THR 3.0 1.4 + - - -
313B ASN* 2.9 25.6 + - - +
409B ASP* 2.9 22.0 - - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B SER* 2.5 39.5 + - - +
281B SER* 3.9 8.5 + - - -
283B THR* 6.2 0.2 - - + -
284B LEU* 3.5 24.9 - - + -
287B THR* 5.6 2.9 - - + -
306B LEU* 2.9 18.5 + - + +
307B PRO 4.9 0.2 - - - +
308B LEU 3.2 0.2 - - - -
309B GLY* 1.3 74.1 - - - +
311B THR* 1.3 62.6 + - - +
313B ASN 4.9 0.4 - - - -
314B MET* 4.3 3.6 - - - +
406B VAL* 5.8 2.2 - - + -
409B ASP* 3.0 17.1 + - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 5.9 4.3 - - + -
64B VAL* 4.0 14.6 - - + +
153B VAL* 3.5 32.3 - - + -
157B ILE* 3.6 14.4 - - + -
281B SER* 4.9 7.8 + - - -
284B LEU* 5.4 3.1 - - - +
307B PRO 3.2 16.4 + - - -
308B LEU 3.0 6.6 + - - -
309B GLY 3.0 0.2 - - - -
310B ALA* 1.3 82.8 + - - +
312B ILE* 1.3 60.8 + - - +
314B MET* 3.4 22.1 - - - +
353B ILE 3.5 6.9 - - - +
355B THR 3.5 10.0 - - - +
357B GLY* 5.4 6.5 - - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B VAL* 5.2 11.0 - - + -
91B TYR* 3.7 27.8 - - + -
92B LEU* 6.1 1.6 - - + -
95B SER* 5.2 1.0 + - - -
154B LEU* 3.7 18.2 - - + -
157B ILE* 3.6 27.8 - - + -
308B LEU* 2.9 36.0 + - + +
311B THR* 1.3 82.4 - - - +
313B ASN* 1.3 64.1 + - - +
314B MET* 3.0 11.6 + - - +
353B ILE* 3.5 46.2 - - + +
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Residues in contact with ASN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 4.5 1.2 - - - -
91B TYR* 3.4 44.0 - - + -
94B THR* 3.8 6.6 + - - -
95B SER* 4.5 3.1 + - - -
309B GLY* 2.9 23.0 + - - +
310B ALA* 4.9 0.2 - - - -
312B ILE* 1.3 76.4 - - - +
314B MET* 1.3 62.5 + - - +
315B ASP* 3.4 24.4 + - - +
405B ASN* 4.2 6.8 + - - +
408B GLY* 3.5 7.3 + - - -
409B ASP* 2.4 51.5 + - - +
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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