Contacts of the strand formed by residues 251 - 256 (chain C) in PDB entry 3G65
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 ALA 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C TYR* 3.4 14.0 - - + -
160C LEU* 2.7 58.4 + - + +
161C PRO 5.0 1.8 - - - +
163C LEU* 5.2 3.6 - - + -
248C PRO* 4.9 10.5 - - + +
250C LYS* 1.3 74.1 - - - +
252C LEU* 1.3 61.9 + - - +
265C LEU* 3.5 15.5 - - + -
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Residues in contact with LEU 252 (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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157C SER* 4.8 11.7 - - - +
158C ILE 3.7 6.7 - - - +
159C TYR* 3.6 45.8 - - + +
160C LEU* 4.8 2.4 - - - +
250C LYS* 3.6 33.7 - - + +
251C ALA* 1.3 75.8 - - - +
253C CYS* 1.3 60.7 + - - +
254C ASN* 3.8 12.6 - - - +
262C HIS 3.6 0.3 - - - +
263C PHE* 3.4 8.0 - - - +
264C ASP* 2.9 49.5 + - + +
265C LEU* 4.5 0.9 - - - +
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Residues in contact with CYS 253 (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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156C VAL 3.5 6.6 - - - +
158C ILE* 2.9 35.0 + - + +
160C LEU* 3.8 23.3 - - + -
182C ILE* 3.9 22.7 - - - -
190C LEU* 5.0 1.6 - - - -
251C ALA 4.3 0.2 + - - -
252C LEU* 1.3 73.7 - - - +
254C ASN* 1.3 62.8 + - - +
255C ILE* 3.4 26.8 + - - +
261C VAL* 4.1 6.1 - - - -
262C HIS 3.6 3.1 - - - -
263C PHE* 3.9 16.4 - - + -
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Residues in contact with ASN 254 (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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151C VAL* 4.1 5.3 - - + +
154C PRO* 3.5 31.5 - - + +
156C VAL 3.3 2.9 - - - -
157C SER* 2.9 32.1 + - - +
252C LEU* 4.3 10.3 - - - +
253C CYS* 1.3 74.9 - - - +
255C ILE* 1.3 60.6 + - - +
256C VAL* 5.3 2.4 - - + +
260C MET 4.1 1.0 - - - +
261C VAL* 3.7 1.6 - - - -
262C HIS* 2.7 70.6 + - + +
264C ASP* 5.2 1.2 - - - +
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Residues in contact with ILE 255 (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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154C PRO* 4.5 0.2 - - - +
155C ASP* 2.9 24.9 + - - +
156C VAL* 2.8 21.9 + - + +
182C ILE* 4.0 23.6 - - + +
184C ALA* 3.7 28.5 - - + -
228C ALA* 3.5 30.7 - - + +
230C VAL* 3.4 26.2 - - + -
253C CYS* 3.7 28.0 - - - +
254C ASN* 1.3 78.7 - - - +
256C VAL* 1.3 66.6 + - - +
260C MET 3.7 2.0 - - - -
261C VAL* 4.5 6.5 - - + -
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Residues in contact with VAL 256 (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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152C PRO* 6.0 7.9 - - + -
153C ASP 4.4 6.7 - - - +
154C PRO* 4.3 15.9 - - + -
155C ASP* 3.5 15.7 - - - +
230C VAL* 4.0 5.0 - - - +
254C ASN 5.3 1.8 - - - +
255C ILE* 1.3 78.8 - - - +
257C ASN* 1.3 56.7 + - - +
258C ASN* 2.6 44.0 + - + +
259C LYS 3.4 9.6 + - - +
260C MET* 3.0 33.6 + - + +
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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