Contacts of the helix formed by residues 304 - 310 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.8 22.8 - - + +
71A GLY* 4.2 5.8 - - - -
72A ALA* 4.5 10.5 - - + -
75A ILE* 3.8 23.8 - - + -
80A LEU* 3.7 25.4 - - + -
83A VAL* 4.4 5.8 - - + -
84A GLY* 4.1 24.2 - - - -
87A ILE* 4.7 4.5 - - + -
161A ILE* 3.5 35.4 - - + -
300A GLY 4.3 3.5 + - - +
301A ILE 4.0 1.8 + - - +
302A PHE 3.4 0.2 - - - -
303A SER* 1.3 79.6 - - - +
305A THR* 1.3 70.1 + - + +
306A LEU 3.4 1.6 - - - -
307A PRO* 3.3 4.8 - - - +
308A LEU* 2.9 43.6 + - + +
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Residues in contact with THR 305 (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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83A VAL* 3.6 29.8 - - + -
87A ILE* 3.8 27.8 - - + -
91A TYR* 3.1 9.8 + - - -
301A ILE* 2.4 27.9 + - + +
302A PHE* 3.9 0.2 - - - -
304A PHE* 1.3 80.9 - - + +
306A LEU* 1.3 57.1 + - - +
308A LEU* 3.0 6.3 + - - +
309A GLY 2.4 34.8 + - - -
413A THR* 2.9 23.6 + - - +
416A VAL* 4.7 6.1 - - + -
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Residues in contact with LEU 306 (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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91A TYR* 5.5 0.7 - - - +
284A LEU* 3.4 7.6 - - + +
287A THR* 3.9 15.7 - - + +
288A MET* 4.3 13.7 - - + -
291A ALA* 3.6 30.3 - - + -
302A PHE* 3.7 14.7 + - + +
305A THR* 1.3 80.9 + - - +
307A PRO* 1.3 70.9 - - + +
309A GLY 4.3 0.4 - - - +
310A ALA* 3.2 26.2 + - - +
409A ASP* 3.5 41.9 - - + +
410A LEU* 3.8 13.0 - - + -
413A THR* 3.6 19.7 - - + +
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Residues in contact with PRO 307 (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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64A VAL* 4.7 1.0 - - - +
67A SER* 3.0 27.8 - - - +
68A LEU* 3.5 22.4 - - + +
197A TYR* 4.5 0.9 - - - +
284A LEU* 4.2 15.8 - - + +
288A MET* 4.5 13.0 - - + -
302A PHE 3.6 4.5 - - - +
303A SER* 3.2 29.2 - - - +
304A PHE* 3.3 15.0 - - - +
306A LEU* 1.3 95.4 - - + +
308A LEU* 1.3 58.4 + - - +
310A ALA* 4.1 4.0 + - - +
311A THR* 3.6 13.5 + - - +
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Residues in contact with LEU 308 (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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68A LEU* 4.1 14.3 - - + +
87A ILE* 4.5 11.0 - - + -
88A VAL* 4.8 8.7 - - + -
91A TYR* 4.2 9.4 - - + -
157A ILE* 3.9 30.1 - - + -
161A ILE* 5.4 3.4 - - + -
304A PHE* 2.9 43.9 + - + +
305A THR* 3.4 4.3 - - - +
307A PRO* 1.3 74.1 - - - +
309A GLY* 1.3 65.4 + - - +
310A ALA 3.1 1.8 - - - -
311A THR* 2.9 20.3 + - - -
312A ILE* 3.1 39.1 + - + +
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Residues in contact with GLY 309 (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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91A TYR* 3.2 26.8 + - - -
305A THR 2.4 17.0 + - - -
306A LEU 4.2 0.2 - - - -
308A LEU* 1.3 71.9 - - - +
310A ALA* 1.3 56.8 + - - +
311A THR 3.1 2.0 + - - -
313A ASN* 2.9 27.9 + - - +
409A ASP* 2.8 27.8 - - - +
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Residues in contact with ALA 310 (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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280A SER* 2.6 37.6 + - - +
281A SER* 3.9 6.7 + - - +
284A LEU* 3.6 28.3 - - + -
287A THR* 5.9 0.9 - - + -
306A LEU 3.2 18.2 + - - +
307A PRO 4.5 1.6 - - - +
308A LEU 3.0 1.4 + - - -
309A GLY* 1.3 74.5 - - - +
311A THR* 1.3 65.5 + - + +
313A ASN 5.3 0.2 - - - -
314A MET* 4.4 4.0 - - - +
357A GLY* 4.5 0.5 - - - -
406A VAL* 6.3 0.9 - - + -
409A ASP* 3.1 12.6 + - - +
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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