Contacts of the strand formed by residues 194 - 200 (chain G) in PDB entry 3HAE
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 TYR 194 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120G LEU* 4.5 2.3 - - + +
135G LEU* 4.2 18.8 - - + -
151G TRP* 5.2 3.6 - - + -
152G LYS 3.5 5.2 - - - -
153G ALA* 3.2 27.6 - - + -
158G VAL* 5.2 5.2 - - + -
181G LEU* 4.2 19.1 - - + -
183G LEU* 3.6 27.9 - - + +
187G GLN* 2.8 22.6 + - - +
188G TRP* 3.6 28.3 - + - -
191G HIS* 2.7 38.7 + + + -
193G SER* 1.3 73.3 - - - +
195G SER* 1.3 67.0 + - - +
208G THR* 3.3 4.5 - - - +
209G VAL* 3.1 38.5 + - + +
211G PRO* 5.8 0.9 - - + -
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Residues in contact with SER 195 (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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150G ALA 3.5 0.9 - - - +
151G TRP* 3.0 29.5 - - - +
152G LYS* 3.1 34.7 + - - +
154G ASP 4.2 6.2 + - - -
193G SER* 4.4 3.8 + - - -
194G TYR* 1.3 77.3 - - - +
196G CYS* 1.3 60.3 + - - +
197G GLN* 3.9 4.0 + - - -
206G GLU* 4.2 11.7 + - - -
207G LYS 3.3 4.3 - - - -
208G THR* 2.9 25.7 - - - +
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Residues in contact with CYS 196 (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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118G VAL* 5.2 0.9 - - + +
120G LEU* 3.5 21.4 - - + +
137G CYS* 2.1 51.1 - - - -
149G VAL* 3.7 19.3 - - - -
150G ALA 3.8 2.7 - - - -
151G TRP* 3.8 13.4 - - + -
195G SER* 1.3 71.4 - - - +
197G GLN* 1.3 63.9 + - - +
198G VAL* 4.2 5.3 - - - +
205G VAL 4.0 1.2 - - - +
206G GLU* 3.8 0.7 - - - -
207G LYS* 2.9 34.7 + - + +
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Residues in contact with GLN 197 (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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148G THR 3.4 1.7 - - - +
149G VAL* 3.3 5.9 - - - -
150G ALA* 3.0 47.3 + - + +
152G LYS* 3.4 39.9 - - + +
195G SER* 4.0 10.8 - - - +
196G CYS* 1.3 78.9 - - - +
198G VAL* 1.3 60.4 + - - +
199G THR* 4.0 3.2 + - - +
204G THR* 4.7 13.9 - - + +
205G VAL 3.8 4.7 - - - +
206G GLU* 3.3 27.7 - - + +
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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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116G PRO* 4.6 8.7 - - + -
118G VAL* 4.1 30.1 - - + -
139G ILE* 3.7 45.5 - - + -
147G VAL* 4.1 15.7 - - + -
148G THR 3.3 3.8 - - - +
149G VAL* 4.2 2.9 - - + -
196G CYS* 4.2 11.7 - - - -
197G GLN* 1.3 76.3 - - - +
199G THR* 1.3 62.3 + - - +
200G HIS* 3.9 1.6 + - - +
203G ASN 4.0 0.7 - - - +
204G THR* 3.2 4.0 - - - +
205G VAL* 2.9 43.8 + - + +
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Residues in contact with THR 199 (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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146G ALA 4.0 0.2 - - - +
147G VAL* 3.2 7.3 - - - -
148G THR* 2.7 54.8 + - - +
197G GLN* 4.7 3.1 + - - +
198G VAL* 1.3 71.1 - - - +
200G HIS* 1.3 62.7 + - - +
202G GLY* 4.7 20.9 - - - +
204G THR* 2.7 22.3 + - - +
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Residues in contact with HIS 200 (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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113G LYS* 4.9 4.9 - - + -
114G ALA 3.6 8.7 - - - -
115G ASN* 4.8 2.2 + - - -
116G PRO* 3.5 34.0 - - + +
142G PHE* 4.1 7.2 - + + -
143G TYR 2.9 35.5 + - - -
144G PRO* 2.8 27.5 + - - +
146G ALA 2.9 26.9 - - - +
147G VAL* 4.2 5.8 - - + -
198G VAL* 3.9 0.8 + - + +
199G THR* 1.3 76.2 - - - +
201G GLU* 1.3 89.7 + - + +
202G GLY 2.9 1.7 + - - -
203G ASN* 2.8 22.5 + - - +
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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