Contacts of the strand formed by residues 191 - 198 (chain G) in PDB entry 3SRF
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 PHE 191 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140G LYS* 4.3 28.3 - - + -
141G ILE 3.2 9.6 - - - +
142G THR* 4.9 3.1 - - + -
143G LEU* 5.9 0.2 - - - -
164G CYS* 4.9 1.1 - - - -
186G GLN* 5.4 3.6 - - + -
187G LYS 4.9 2.9 - - - -
188G GLY* 2.9 50.4 + - - +
189G ALA* 3.7 6.7 - - + -
190G ASP* 1.3 93.5 - - - +
192G LEU* 1.3 70.5 + - - +
193G VAL* 4.5 21.1 - - + -
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Residues in contact with LEU 192 (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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139G LEU 3.8 0.2 - - - +
140G LYS* 3.3 5.8 - - - -
141G ILE* 2.8 50.5 + - + +
143G LEU* 6.1 1.8 - - + -
158G LEU* 6.3 0.2 - - + -
163G ILE* 4.9 19.1 - - + +
164G CYS* 5.3 9.0 - - - -
167G VAL* 3.8 26.9 - - + -
173G ILE* 4.8 8.5 - - + -
184G VAL* 3.8 22.7 - - + -
186G GLN 3.6 13.2 - - - +
187G LYS* 3.8 22.2 - - + -
191G PHE* 1.3 80.9 - - - +
193G VAL* 1.3 63.0 + - - +
194G THR* 3.5 13.0 + - + +
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Residues in contact with VAL 193 (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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138G THR* 4.5 14.1 - - - +
139G LEU 4.3 2.0 - - - -
140G LYS* 4.6 12.3 - - + +
184G VAL* 3.7 0.5 - - - -
185G LYS* 2.7 47.6 + - + +
186G GLN* 3.0 37.4 + - + +
191G PHE* 4.5 17.2 - - + -
192G LEU* 1.3 70.3 - - - +
194G THR* 1.3 57.4 + - - +
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Residues in contact with THR 194 (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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138G THR* 3.8 3.8 + - - -
139G LEU* 2.6 54.5 + - - +
141G ILE* 3.8 23.1 - - + +
173G ILE* 5.0 2.0 - - + -
182G LEU* 3.8 29.8 - - + +
183G GLN 3.1 12.8 - - - +
184G VAL* 3.8 21.3 - - + -
185G LYS* 4.3 2.7 - - - -
192G LEU* 4.2 8.3 - - + +
193G VAL* 1.3 81.4 - - - +
195G GLU* 1.3 60.8 + - - +
196G VAL 4.1 0.3 + - - -
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Residues in contact with GLU 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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136G GLY* 3.8 20.0 - - - +
137G ALA 3.5 16.4 - - - +
138G THR* 4.8 1.3 - - - +
182G LEU* 3.4 1.5 - - - -
183G GLN 2.9 31.9 + - - -
185G LYS* 3.5 39.1 + - + +
194G THR* 1.3 72.6 - - - +
196G VAL* 1.3 63.9 + - - +
197G GLU* 3.1 18.0 + - - +
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Residues in contact with VAL 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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133G LEU* 3.8 24.0 - - + -
134G LYS 4.1 14.4 - - - +
136G GLY* 2.9 32.9 + - - -
137G ALA* 3.1 21.9 + - + +
138G THR 5.2 0.2 - - - +
139G LEU* 4.1 14.4 - - + -
180G ILE* 4.5 0.7 - - + -
181G SER 3.4 9.2 - - - +
182G LEU* 3.7 19.5 - - + -
195G GLU* 1.3 69.0 - - - +
197G GLU* 1.3 59.9 + - - +
198G ASN 3.4 29.6 - - - +
199G GLY* 4.0 9.6 - - - +
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Residues in contact with GLU 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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135G LYS* 3.6 17.2 + - - +
172G LYS* 5.0 10.8 + - + +
181G SER* 2.9 31.5 + - - +
182G LEU 4.2 0.7 - - - +
183G GLN* 3.0 43.6 - - + +
185G LYS* 4.9 0.2 + - - -
195G GLU* 3.1 21.5 + - - +
196G VAL* 1.3 73.6 - - - +
198G ASN* 1.3 66.8 + - - +
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Residues in contact with ASN 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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135G LYS* 4.0 20.2 - - - +
174G TYR* 5.5 2.0 - - - -
178G GLY 5.0 1.7 - - - +
179G LEU 3.0 21.3 - - - +
180G ILE* 3.7 2.3 - - - +
181G SER* 3.2 36.2 + - - -
196G VAL* 3.3 13.4 - - - +
197G GLU* 1.3 83.8 + - - +
199G GLY* 1.3 65.5 - - - +
337H PRO* 5.6 11.0 - - + -
338H ARG* 5.8 3.1 + - - +
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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