Contacts of the strand formed by residues 180 - 187 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU* 5.0 13.7 - - + -
173A ILE 3.6 1.0 - - - +
174A TYR* 3.2 8.7 - - - +
175A VAL* 2.8 51.8 + - + +
176A ASP* 4.4 6.3 - - + +
179A LEU* 1.3 85.6 - - + +
181A SER* 1.3 68.1 + - - +
182A LEU* 4.7 11.4 - - + -
196A VAL* 5.2 2.0 - - + -
198A ASN* 3.6 14.4 - - - +
199A GLY 4.4 9.9 - - - +
200A GLY* 4.5 7.6 - - - +
201A SER 3.8 24.2 - - - +
202A LEU* 3.9 31.0 - - + -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS* 4.1 12.1 + - - +
173A ILE 3.7 2.9 - - - -
174A TYR* 4.0 19.7 + - - -
180A ILE* 1.3 74.3 - - - +
182A LEU* 1.3 74.1 + - - +
196A VAL* 4.0 1.6 - - - +
197A GLU* 3.1 38.0 + - - +
198A ASN* 2.9 36.8 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.6 6.5 - - + -
139A LEU* 3.9 26.9 - - + -
141A ILE* 3.9 26.7 - - + -
156A LEU* 4.5 3.1 - - + -
172A LYS* 3.2 12.6 - - - +
173A ILE* 2.9 42.2 + - + +
175A VAL* 4.1 24.2 - - + -
180A ILE* 4.7 8.3 - - + -
181A SER* 1.3 83.6 + - - +
183A GLN* 1.3 63.7 + - - +
194A THR* 4.3 11.4 - - + +
195A GLU 3.6 6.1 - - - +
196A VAL* 4.2 19.5 - - + -
197A GLU* 4.2 2.5 - - - -
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY* 3.0 38.3 + - - +
171A SER 3.3 7.4 - - - +
172A LYS* 3.4 26.9 - - + +
182A LEU* 1.3 76.9 - - - +
184A VAL* 1.3 64.5 + - - +
185A LYS* 3.4 21.9 + - - +
194A THR* 3.2 5.4 - - - -
195A GLU* 2.8 36.2 + - - +
197A GLU* 3.5 27.8 - - + +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A VAL* 4.1 16.6 - - + -
168A GLU 3.9 15.0 - - - +
169A VAL* 4.7 3.9 - - - +
170A GLY* 3.2 25.3 + - - +
171A SER 3.1 16.2 + - - +
173A ILE* 3.9 22.9 - - + -
183A GLN* 1.3 70.8 - - - +
185A LYS* 1.3 70.2 + - - +
186A GLN 3.6 24.9 - - - +
187A LYS* 4.3 5.8 - - + +
192A LEU* 3.9 19.5 - - + -
193A VAL 4.3 1.3 - - - +
194A THR* 3.7 11.4 - - + -
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A VAL* 4.0 17.4 - - - +
170A GLY* 5.7 0.2 - - - -
183A GLN* 3.8 29.0 + - - +
184A VAL* 1.3 92.1 - - - +
186A GLN* 1.3 79.3 + - - +
187A LYS 4.3 0.2 + - - -
193A VAL* 2.8 17.0 + - + +
194A THR 4.3 0.9 - - - -
195A GLU* 3.2 53.1 + - + +
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.6 8.4 - - - +
185A LYS* 1.3 100.9 + - - +
187A LYS* 1.3 61.4 + - - +
191A PHE* 4.3 7.6 - - + +
192A LEU* 3.5 5.5 - - - -
193A VAL* 3.0 62.2 + - + +
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A CYS* 3.2 22.7 + - + +
165A LYS* 5.2 1.0 - - - +
167A VAL* 2.9 33.4 + - - -
168A GLU* 4.1 22.2 + - - +
169A VAL* 4.7 18.0 - - + +
184A VAL* 4.3 5.3 - - + +
185A LYS 4.3 0.8 + - - -
186A GLN* 1.3 76.2 - - - +
188A GLY* 1.3 69.8 + - - +
191A PHE* 5.0 2.7 - - - -
192A LEU* 3.8 19.3 - - + -
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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