Contacts of the helix formed by residues 298 - 303 (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 ASP 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ARG* 5.8 4.8 + - - +
292A GLU* 4.5 4.6 - - - +
297A VAL* 1.3 74.9 - - - +
299A LYS* 1.3 92.4 + - - +
300A GLY 3.1 5.3 + - - +
301A ILE* 3.1 19.3 + - + +
302A PHE* 3.1 12.5 + - - -
422A GLU* 3.4 40.4 + - + +
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Residues in contact with LYS 299 (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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292A GLU* 4.4 15.2 + - - +
298A ASP* 1.3 88.9 + - - +
300A GLY* 1.3 56.9 + - - +
302A PHE* 3.4 21.2 - - + -
303A SER* 2.9 41.6 + - - -
175C GLU* 4.1 6.8 + - - -
177C ARG* 3.6 39.3 - - - +
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Residues in contact with GLY 300 (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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74A SER* 5.3 4.3 - - - -
75A ILE* 3.1 35.7 - - - +
79A ARG* 3.9 27.1 - - - +
83A VAL* 5.3 4.0 - - - +
298A ASP* 3.1 5.7 + - - +
299A LYS* 1.3 79.3 - - - +
301A ILE* 1.3 63.4 + - - +
303A SER* 5.2 0.4 - - - -
304A PHE* 4.3 4.7 + - - +
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Residues in contact with ILE 301 (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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79A ARG* 5.0 4.0 - - - +
83A VAL* 4.9 5.2 - - + -
297A VAL* 4.8 4.3 - - + -
298A ASP* 3.1 20.7 + - + +
300A GLY* 1.3 84.5 - - - +
302A PHE* 1.3 53.5 + - - +
303A SER 3.5 0.4 - - - -
304A PHE 4.4 0.4 - - - -
305A THR* 2.4 41.9 + - + +
413A THR* 4.0 20.0 - - - +
416A VAL* 4.0 26.0 - - + -
417A ALA* 4.0 15.0 - - + +
420A GLU* 3.3 24.0 - - - +
422A GLU* 3.5 39.3 - - + +
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Residues in contact with PHE 302 (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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288A MET* 3.2 57.9 - - + +
291A ALA* 4.1 5.2 - - + -
292A GLU* 3.6 21.3 - - + -
297A VAL* 3.4 35.7 - - + -
298A ASP 3.1 21.7 + - - -
299A LYS* 3.4 32.3 - - + -
301A ILE* 1.3 76.6 - - - +
303A SER* 1.3 62.9 + - - +
304A PHE 3.4 1.3 - - - -
305A THR* 3.9 5.8 - - - -
306A LEU* 3.7 17.2 - - + +
307A PRO* 3.6 14.1 - - - +
413A THR* 4.1 2.7 - - - +
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Residues in contact with SER 303 (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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67A SER* 4.0 3.1 + - - +
70A VAL* 4.8 8.7 - - - +
71A GLY* 3.3 25.8 + - - -
74A SER* 5.5 5.3 - - - -
75A ILE* 6.5 0.2 - - - -
288A MET* 4.9 10.2 - - - +
299A LYS* 2.9 29.1 + - - -
300A GLY* 5.2 0.4 - - - -
302A PHE* 1.3 80.2 - - - +
304A PHE* 1.3 58.5 + - - +
307A PRO* 3.2 18.5 - - - +
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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