Contacts of the strand formed by residues 195 - 201 (chain G) in PDB entry 3DUF
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 195 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G ALA* 4.5 9.4 - - + +
155G ALA* 3.8 15.9 - - + -
167G ALA* 3.3 9.9 - - + +
188G ALA* 4.7 3.8 - - + -
193G ALA 3.1 8.7 + - - +
194G PRO* 1.3 76.1 - - - +
196G ILE* 1.3 64.3 + - - +
197G PHE* 3.9 27.8 + - + -
252G ALA* 4.8 1.4 - - - +
258G PRO* 3.2 27.2 - - + +
259G THR 3.3 3.1 + - - -
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Residues in contact with ILE 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 4.7 4.7 - - + -
166G VAL* 4.2 19.3 - - + -
167G ALA 2.8 13.9 + - - +
168G ILE* 3.5 9.6 - - + +
169G THR* 3.2 26.3 + - - +
195G ALA* 1.3 74.8 - - - +
197G PHE* 1.3 62.4 + - - +
198G VAL* 3.7 20.7 + - + -
245G VAL* 4.1 15.7 - - + +
248G ALA* 4.1 18.4 - - + +
249G ARG* 3.8 35.4 - - + +
252G ALA* 5.0 2.9 - - + -
259G THR* 3.8 5.2 - - - +
261G ILE* 4.0 21.1 - - + -
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Residues in contact with PHE 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G TYR* 3.7 43.3 - + + +
151G ALA* 4.1 12.3 - - + -
152G ALA 5.0 2.2 - - - -
169G THR* 3.7 17.9 - - + -
184G GLY 3.8 12.1 - - - -
185G ILE* 3.9 19.1 - - + -
188G ALA* 3.6 32.8 - - + -
195G ALA* 3.9 15.9 - - + -
196G ILE* 1.3 71.9 - - - +
198G VAL* 1.3 54.7 + - - +
228G ILE* 4.7 2.7 - - + -
258G PRO* 3.8 14.6 - - + -
259G THR 2.8 22.0 + - - +
260G LEU* 3.3 19.3 - - + +
261G ILE* 2.8 33.8 + - - +
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Residues in contact with VAL 198 (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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84G SER 5.0 2.2 - - - +
88G SER* 5.5 2.7 - - - -
148G TYR* 3.2 7.7 + - - -
168G ILE* 4.1 17.3 - - + -
169G THR 3.0 15.4 + - - +
170G TYR* 3.3 26.8 - - + -
171G THR 3.1 22.5 + - - +
196G ILE* 3.9 19.7 - - + -
197G PHE* 1.3 76.9 - - - +
199G VAL* 1.3 62.0 + - - +
200G GLN* 4.1 13.2 + - + +
245G VAL* 5.0 6.7 - - + -
261G ILE* 3.5 18.2 - - + +
263G THR* 4.2 14.6 - - + -
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Residues in contact with VAL 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G TYR* 3.4 19.5 - - - +
171G THR* 3.4 9.6 - - + +
172G GLY 4.1 11.2 - - - +
173G ASP 4.3 0.7 - - - +
176G THR* 3.8 21.3 - - + -
181G PHE* 3.9 14.4 - - + -
198G VAL* 1.3 73.0 - - - +
200G GLN* 1.3 61.3 + - - +
201G ASN 3.4 4.0 + - - +
219G LEU* 4.2 20.6 - - + +
260G LEU* 3.8 22.0 - - + -
261G ILE 2.8 12.6 + - - +
262G GLU* 3.4 9.2 - - + +
263G THR* 2.9 28.2 + - - -
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Residues in contact with GLN 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLN* 3.9 14.3 + - - +
84G SER* 3.3 23.8 + - - +
85G GLN* 3.3 27.7 + - - +
103G ARG* 5.9 1.0 - - - +
104G ASP* 3.1 19.3 + - - +
170G TYR* 3.6 21.9 - - + +
171G THR 2.8 18.7 + - - +
172G GLY* 3.9 8.4 - - - -
173G ASP* 3.7 5.6 - - - +
198G VAL* 4.2 11.0 - - + -
199G VAL* 1.3 74.8 - - - +
201G ASN* 1.3 58.3 + - - +
202G ASN* 3.1 14.4 + - - -
263G THR* 3.5 15.7 - - - +
265G CYS* 3.9 12.4 - - - -
1370G R1T 5.1 1.1 + - - +
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Residues in contact with ASN 201 (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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173G ASP* 3.4 14.2 - - - +
199G VAL* 3.4 2.2 + - - +
200G GLN* 1.3 69.0 - - - +
202G ASN* 1.3 57.6 + - - +
203G ARG* 2.8 44.0 + - - +
210G VAL* 4.3 13.5 - - - +
219G LEU* 3.5 25.9 - - + +
262G GLU* 3.2 23.7 + - + +
263G THR 3.0 15.7 + - - +
264G LEU* 3.8 14.7 - - + +
265G CYS* 3.0 25.7 + - - +
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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