Contacts of the strand formed by residues 178 - 187 (chain A) in PDB entry 4S0H
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 LYS 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 5.5 4.0 - - - -
108A PRO* 3.8 4.2 - - - +
109A ALA* 3.0 35.5 + - + -
110A ASP* 3.6 27.8 + - - +
114A TYR* 3.8 28.1 - - + +
177A HIS* 1.3 78.1 - - - +
179A TYR* 1.3 63.8 + - - +
210A ALA* 5.6 7.7 + - - -
211A PHE* 3.2 10.4 - - - +
212A ILE* 3.5 38.6 - - + +
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Residues in contact with TYR 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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106A ILE* 3.5 20.9 - - + -
107A VAL* 3.5 4.5 - - - -
108A PRO* 4.1 22.9 - - + -
109A ALA* 3.9 4.0 - - - +
130A ALA* 4.5 1.0 - - + +
131A MET* 1.7 46.7 - - + +
173A LEU* 3.6 20.2 - - + -
174A ASN* 2.6 28.2 + - - +
177A HIS* 3.3 36.4 - - + +
178A LYS* 1.3 75.0 - - - +
180A GLN* 1.3 62.2 + - - +
181A PRO* 4.3 1.6 - - - -
210A ALA* 3.2 8.3 - - - +
211A PHE* 2.7 45.9 + + + -
213A ALA* 3.8 16.2 - - + -
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Residues in contact with GLN 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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106A ILE* 4.3 1.6 - - - -
107A VAL* 2.7 48.4 + - + +
108A PRO 4.9 0.7 - - - +
109A ALA* 4.5 13.1 - - + +
179A TYR* 1.3 78.1 - - - +
181A PRO* 1.3 98.8 + - - +
182A ARG* 3.6 2.5 + - + -
205A VAL* 3.2 29.8 - - + +
206A PHE 3.5 1.8 + - - -
207A PRO* 3.7 10.9 - - - +
209A THR* 3.3 13.3 + - - -
210A ALA* 3.2 22.0 - - - +
189E ASP* 5.8 0.9 - - - +
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Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 5.9 0.7 - - + -
83A MET* 5.0 7.9 - - - -
87A TYR* 4.0 14.9 + - + -
104A MET* 3.8 23.6 - - + -
105A ASP 3.4 6.3 - - - +
106A ILE* 4.4 7.2 - - + -
179A TYR 4.1 1.6 - - - +
180A GLN* 1.3 110.8 + - - +
182A ARG* 1.3 61.6 + - - +
204A HIS 4.3 2.4 - - - +
205A VAL* 4.2 5.7 - - - +
206A PHE 4.6 0.9 + - - -
209A THR* 3.2 36.8 + - - +
211A PHE* 4.1 16.8 - - + -
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Residues in contact with ARG 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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104A MET* 3.4 8.1 - - - +
105A ASP* 2.6 67.4 + - - +
107A VAL* 3.5 24.3 - - + +
180A GLN* 3.9 11.0 - - + +
181A PRO* 1.3 79.0 - - - +
183A LEU* 1.3 59.7 + - - +
184A HIS* 3.9 7.9 + - - +
203A THR* 3.9 21.4 - - + +
204A HIS 3.8 4.3 - - - -
205A VAL* 4.0 16.6 - - + -
186E VAL* 3.2 15.0 - - - +
187E LYS* 3.2 39.1 + - - +
188E ALA* 4.6 3.0 - - - +
189E ASP 5.5 0.6 - - - +
201E PHE* 3.3 26.9 - - - -
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Residues in contact with LEU 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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56A VAL* 4.1 36.1 - - + -
87A TYR* 3.9 20.6 + - + +
89A VAL* 4.6 9.9 - - + -
91A VAL* 5.0 0.7 - - + -
102A LEU* 3.9 21.3 - - + -
103A LEU 3.5 11.4 - - - +
104A MET* 4.6 1.8 - - + -
155A PHE* 3.5 35.0 - - + -
182A ARG* 1.3 74.1 - - - +
184A HIS* 1.3 63.8 + - - +
185A ILE* 4.2 13.6 + - + -
202A CYS 3.8 0.5 - - - +
203A THR* 3.3 8.0 - - - +
204A HIS* 3.2 37.3 + - + +
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Residues in contact with HIS 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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101A ILE 3.6 1.0 - - - +
102A LEU* 3.3 5.0 - - - -
103A LEU* 2.8 52.7 + - + +
104A MET 4.6 0.2 - - - -
105A ASP* 3.2 37.6 + - + +
135A LEU* 5.2 3.7 - - + +
182A ARG* 3.9 15.8 - - - +
183A LEU* 1.3 78.2 - - - +
185A ILE* 1.3 62.6 + - - +
186A VAL* 3.8 6.9 + - + -
201A PHE* 3.7 25.9 - + + -
202A CYS 3.4 4.0 - - - -
203A THR* 2.9 30.6 + - + -
186E VAL* 4.0 9.1 - - + +
201E PHE* 3.9 18.4 - + - -
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Residues in contact with ILE 185 (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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54A ILE* 4.3 12.3 - - + -
56A VAL* 4.5 4.5 - - + -
91A VAL* 3.9 28.0 - - + -
94A LEU* 4.2 14.6 - - + -
100A TYR* 3.6 36.1 - - + -
101A ILE 3.6 2.0 - - - -
102A LEU* 3.6 26.2 - - + -
183A LEU* 4.2 18.6 - - + +
184A HIS* 1.3 74.3 - - - +
186A VAL* 1.3 61.4 + - - +
201A PHE* 3.0 17.7 - - - +
202A CYS* 3.1 30.0 + - - -
204A HIS* 4.8 1.3 - - + -
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Residues in contact with VAL 186 (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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100A TYR* 3.3 7.7 - - - +
101A ILE* 2.6 49.0 + - + +
103A LEU* 3.7 29.4 - - + -
184A HIS* 4.3 2.9 - - + -
185A ILE* 1.3 75.5 - - - +
187A LYS* 1.3 71.8 + - - +
201A PHE* 3.4 44.0 - - + -
182E ARG* 4.1 15.0 - - - +
184E HIS* 4.2 10.3 - - + +
203E THR* 4.8 0.7 - - - +
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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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98A THR* 4.6 12.6 - - + -
99A LYS 3.7 7.0 - - - +
100A TYR* 4.0 25.1 - - + -
101A ILE* 4.6 0.9 - - - -
186A VAL* 1.3 76.2 - - - +
188A ALA* 1.3 62.3 + - - +
200A ALA* 5.2 20.2 - - + +
201A PHE* 5.0 1.8 - - - +
182E ARG* 2.8 31.4 + - - +
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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