Contacts of the strand formed by residues 244 - 247 (chain G) in PDB entry 4D1Q
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 LYS 244 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173G ASP* 3.1 29.2 + - - +
174G GLY 3.4 0.6 - - - -
175G ALA 3.2 36.1 + - - +
176G SER* 3.2 8.4 + - - +
177G ALA 2.9 23.6 + - - -
242G SER 3.8 12.8 - - - +
243G ILE* 1.3 71.9 - - - +
245G PHE* 1.3 60.9 + - - +
246G VAL 4.1 0.2 + - - -
261G ILE* 4.0 11.9 - - + -
263G ILE* 4.5 5.6 - - + -
428G TRP* 3.5 37.5 - - + -
457G LYS* 6.4 0.9 - - - +
560G SER* 3.4 19.6 + - - +
564G ILE* 3.3 32.1 - - + +
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Residues in contact with PHE 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ALA* 3.2 36.8 - - + +
179G ILE* 4.6 10.8 - - + -
228G LEU* 4.2 20.2 - - + -
232G PHE* 4.4 7.4 - + - -
240G LEU* 3.5 36.6 - - + -
243G ILE* 3.6 25.6 - - + -
244G LYS* 1.3 70.8 - - - +
246G VAL* 1.3 54.6 + - - +
247G THR* 3.9 2.2 - - - +
257G LEU* 3.9 31.2 - - + -
260G ASN* 4.0 14.8 - - + -
261G ILE 3.2 25.8 + - - +
262G ARG* 3.0 7.2 - - + +
263G ILE* 2.7 33.9 + - - +
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Residues in contact with VAL 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ALA 2.8 11.9 + - - +
178G THR* 3.3 32.2 - - - +
179G ILE 3.5 4.7 + - - -
244G LYS 5.0 0.9 - - - +
245G PHE* 1.3 72.1 - - - +
247G THR* 1.3 64.3 + - - +
263G ILE* 3.7 20.9 - - + +
264G ASN 4.8 0.2 - - - -
265G CYS* 4.3 5.8 - - - +
564G ILE* 4.1 6.3 - - + -
565G PRO* 3.3 44.4 - - + +
566G ALA 4.3 2.5 - - - +
567G SER* 3.6 33.4 - - - +
568G SER* 3.8 2.0 - - - +
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Residues in contact with THR 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G ILE* 3.6 22.0 - - - +
245G PHE* 3.9 1.4 - - - +
246G VAL* 1.3 73.7 + - - +
248G ASP* 1.3 87.7 + - - +
250G GLY 5.1 0.2 - - - +
253G VAL* 3.8 24.7 - - + -
254G VAL* 4.6 2.2 - - + -
257G LEU* 3.6 20.1 - - - +
262G ARG* 3.6 23.7 - - - +
263G ILE 3.2 7.2 + - - +
264G ASN 3.5 0.2 - - - -
265G CYS* 2.6 39.0 + - - +
568G SER* 4.2 2.7 - - - -
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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
------------------------------------------------------------
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