Contacts of the strand formed by residues 174 - 182 (chain A) in PDB entry 5IFM
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 VAL 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 3.2 25.3 - - - +
165A GLU* 3.7 30.5 - - + +
168A PHE* 3.7 6.5 - - + -
169A SER* 3.5 35.5 - - - +
172A GLY 3.5 0.2 + - - -
173A GLN* 1.4 74.8 - - - +
175A GLU* 1.3 62.5 + - - +
176A ARG 3.6 18.4 - - - +
177A ALA* 4.4 5.8 - - + +
193A VAL* 4.4 3.6 - - + -
194A GLU 3.6 12.1 - - - +
195A PHE* 3.6 21.3 - - + -
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Residues in contact with GLU 175 (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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68A LYS* 2.9 35.2 + - + +
71A THR* 3.5 24.0 - - + +
72A GLN* 2.8 38.6 + - - +
73A ARG* 4.3 3.3 + - + +
115A ARG* 4.1 2.9 + - - -
146A HIS* 2.7 27.8 + - - -
173A GLN 3.9 1.4 + - - -
174A VAL* 1.3 71.3 - - - +
176A ARG* 1.3 61.7 + - + +
194A GLU* 2.7 19.2 + - + +
195A PHE 3.7 9.6 - - - -
196A SER* 3.6 26.4 - - - +
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Residues in contact with ARG 176 (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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68A LYS* 4.8 2.5 - - - +
73A ARG* 3.7 43.9 - - + +
165A GLU* 4.9 2.0 - - - -
174A VAL* 3.6 5.9 - - - +
175A GLU* 1.3 81.0 - - + +
177A ALA* 1.3 64.6 + - - +
178A VAL* 3.4 21.5 - - + +
192A ILE* 4.0 19.7 - - - +
193A VAL* 3.7 0.5 - - - -
194A GLU* 2.8 77.7 + - - +
232B ASP* 3.3 24.4 + - - -
233B GLU* 4.1 10.6 + - - +
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Residues in contact with ALA 177 (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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161A ASN* 3.6 25.3 + - - +
164A LEU* 3.9 11.7 - - + -
165A GLU* 3.6 42.1 + - + +
174A VAL* 4.4 2.9 - - + +
176A ARG* 1.3 76.5 - - - +
178A VAL* 1.3 66.1 + - - +
192A ILE 3.1 10.1 - - - +
193A VAL* 4.4 5.6 - - + -
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Residues in contact with VAL 178 (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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161A ASN* 3.6 6.1 - - - +
164A LEU* 3.4 7.1 - - - +
176A ARG* 3.4 42.4 - - + +
177A ALA* 1.3 79.2 - - - +
179A VAL* 1.3 64.8 + - - +
180A ILE* 3.7 1.4 + - - +
191A GLY* 3.1 5.9 - - - -
192A ILE* 2.8 42.1 + - + -
232B ASP* 3.6 25.6 - - - +
233B GLU 4.2 7.2 - - - +
234B GLU 4.5 0.9 - - - -
235B GLY* 3.7 26.2 - - - +
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Residues in contact with VAL 179 (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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155A LEU* 4.6 13.0 - - + -
159A VAL* 3.7 33.0 - - + +
160A SER 3.5 30.7 - - - +
161A ASN* 2.8 12.7 + - - +
164A LEU* 4.1 7.4 - - + -
178A VAL* 1.3 72.3 - - - +
180A ILE* 1.3 69.6 - - - +
181A VAL* 4.1 0.2 - - - +
187A PRO* 3.9 16.8 - - + -
190A LYS 4.1 3.1 - - - +
191A GLY* 4.4 0.9 - - - -
235B GLY* 3.0 24.9 - - - -
236B LEU* 3.3 16.7 + - + -
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Residues in contact with ILE 180 (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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178A VAL* 4.5 1.8 - - + +
179A VAL* 1.3 75.7 - - - +
181A VAL* 1.3 61.0 + - - +
187A PRO* 3.5 6.4 - - - +
188A SER* 3.1 33.3 + - - +
190A LYS* 3.0 32.4 + - + +
191A GLY* 4.0 9.9 - - - +
192A ILE* 3.8 27.6 - - + -
230B LEU* 3.7 34.5 - - + -
231B ASP 3.6 10.1 - - - +
232B ASP* 4.0 20.4 - - + +
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Residues in contact with VAL 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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179A VAL 4.1 1.3 - - - +
180A ILE* 1.3 79.1 - - - +
182A ASP* 1.3 71.1 + - - +
185A GLY* 3.5 33.2 - - - +
186A ARG 3.5 7.9 - - - +
187A PRO* 3.8 7.9 - - + -
188A SER 4.3 0.4 - - - +
230B LEU* 3.3 7.7 - - - -
231B ASP* 2.7 51.2 + - + +
234B GLU* 5.7 0.9 - - - +
235B GLY 4.1 16.2 - - - +
236B LEU* 4.0 25.4 - - + -
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Residues in contact with ASP 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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181A VAL* 1.3 81.8 - - - +
183A ASP* 1.3 61.2 + - - +
184A ARG* 2.9 42.2 + - - +
185A GLY 3.0 9.0 + - - -
186A ARG* 3.0 60.8 + - - +
187A PRO 5.4 0.7 - - - +
188A SER* 4.9 1.9 - - - +
228B ASP* 5.5 2.7 - - - +
229B GLN 3.6 11.0 - - - +
230B LEU* 4.2 12.5 - - + +
231B ASP* 5.1 3.0 - - - +
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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