Contacts of the strand formed by residues 180 - 187 (chain C) 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 ILE 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C LEU* 4.0 22.2 - - + -
173C ILE 4.0 0.4 - - - +
174C TYR* 3.4 7.8 - - - +
175C VAL* 2.9 50.6 + - + +
176C ASP* 4.4 10.5 - - + +
178C GLY 4.2 0.8 - - - +
179C LEU* 1.3 81.8 - - + +
181C SER* 1.3 62.9 + - - +
182C LEU* 4.0 16.6 - - + -
196C VAL* 5.1 0.7 - - + -
198C ASN 4.0 9.6 - - - +
199C GLY 4.5 10.5 - - - +
200C GLY* 4.6 6.7 - - - +
201C SER 3.5 25.6 - - - +
202C LEU* 4.0 30.3 - - + -
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Residues in contact with SER 181 (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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172C LYS* 4.6 3.8 + - - +
173C ILE 3.8 2.5 - - - -
174C TYR* 3.3 31.7 + - - -
178C GLY 5.3 0.9 - - - -
179C LEU 5.1 0.2 - - - -
180C ILE* 1.3 76.3 - - - +
182C LEU* 1.3 67.9 + - - +
196C VAL* 3.7 0.9 - - - -
197C GLU* 2.8 41.6 + - - +
198C ASN* 3.3 35.3 + - - +
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Residues in contact with LEU 182 (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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139C LEU* 3.9 26.0 - - + -
141C ILE* 4.2 12.8 - - + -
156C LEU* 5.0 2.2 - - + -
172C LYS* 3.3 11.6 - - - +
173C ILE* 2.8 61.1 + - + +
175C VAL* 4.1 14.6 - - + -
180C ILE* 4.0 17.3 - - + -
181C SER* 1.3 85.0 + - - +
183C GLN* 1.3 61.5 + - - +
194C THR* 4.0 22.4 - - - +
195C GLU 3.5 4.0 - - - -
196C VAL* 4.2 17.0 - - + -
197C GLU* 3.7 4.3 - - - -
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Residues in contact with GLN 183 (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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170C GLY* 3.4 27.1 + - - +
171C SER 3.5 2.5 - - - +
172C LYS* 3.5 19.9 - - - +
182C LEU* 1.3 75.3 - - - +
184C VAL* 1.3 71.3 + - - +
185C LYS* 3.3 27.8 + - - +
194C THR* 3.1 5.1 - - - -
195C GLU* 2.8 40.7 + - + +
197C GLU* 3.6 26.0 + - - +
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Residues in contact with VAL 184 (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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167C VAL* 4.2 12.1 - - + -
168C GLU 4.1 17.0 - - - +
169C VAL* 4.4 7.2 - - - +
170C GLY* 3.1 22.3 + - - -
171C SER* 3.1 16.1 + - - +
173C ILE* 3.7 29.6 - - + -
183C GLN* 1.3 69.8 - - - +
185C LYS* 1.3 73.2 + - - +
186C GLN 4.1 15.9 - - - +
187C LYS* 4.5 3.1 - - + +
192C LEU* 3.9 26.7 - - + -
193C VAL 3.7 5.8 - - - +
194C THR* 3.8 7.4 - - + -
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Residues in contact with LYS 185 (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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169C VAL* 3.5 21.9 - - - +
170C GLY* 5.3 2.7 - - - -
183C GLN* 3.3 40.5 + - - +
184C VAL* 1.3 93.0 - - - +
186C GLN* 1.3 83.6 + - - +
193C VAL* 2.8 15.1 + - + +
194C THR 4.7 1.1 - - - -
195C GLU* 4.1 28.9 - - + +
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Residues in contact with GLN 186 (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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184C VAL* 4.1 5.5 - - - +
185C LYS* 1.3 101.8 + - - +
187C LYS* 1.3 62.3 + - - +
191C PHE* 4.6 4.7 - - + -
192C LEU* 3.7 2.9 - - - -
193C VAL* 2.9 62.9 + - + +
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Residues in contact with LYS 187 (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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164C CYS* 3.8 18.3 + - + +
167C VAL* 3.4 19.9 + - + -
168C GLU* 2.7 40.9 + - - +
169C VAL* 4.4 20.2 - - + +
184C VAL* 4.5 5.3 - - + +
185C LYS 4.3 0.2 - - - -
186C GLN* 1.3 76.1 - - - +
188C GLY* 1.3 69.2 + - - +
191C PHE* 4.0 8.6 - - - -
192C LEU* 4.0 20.0 - - + -
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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