Contacts of the strand formed by residues 172 - 181 (chain A) in PDB entry 5B82
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 LEU 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.8 32.8 - - + +
112A PHE* 4.0 12.8 - - + -
113A ASP* 3.8 29.4 - - + +
134A ARG* 4.0 27.5 - - + +
135A ILE 3.7 6.1 - - - +
136A ASP* 3.9 6.7 - - - +
167A PHE* 3.7 13.0 - - - -
170A GLY 3.8 0.8 + - - -
171A ASP* 1.3 72.5 - - - +
173A ARG* 1.3 59.2 + - - +
174A GLY* 3.4 28.5 - - - +
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Residues in contact with ARG 173 (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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90A ALA* 3.4 14.7 - - - +
91A LEU 5.0 1.2 + - - -
92A LYS 2.9 24.8 + - - +
135A ILE* 2.8 30.7 + - + +
136A ASP 4.2 1.6 - - - -
137A VAL* 3.8 18.2 - - + -
141A CYS* 6.3 0.2 - - - -
145A HIS* 3.2 32.1 + - - -
164A ALA* 3.3 9.8 - - - +
167A PHE* 3.8 28.9 - - - -
171A ASP 3.4 2.4 + - - -
172A LEU* 1.3 72.8 - - - +
174A GLY* 1.3 55.6 + - - +
501A HEC 2.7 73.9 + - + +
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Residues in contact with GLY 174 (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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89A VAL 3.3 13.5 - - - -
90A ALA* 4.0 6.3 - - - -
91A LEU 5.4 0.2 - - - -
109A LEU* 4.2 11.2 - - - -
134A ARG* 3.8 0.3 - - - -
135A ILE* 2.8 26.3 + - - +
172A LEU* 3.4 13.7 - - - +
173A ARG* 1.3 80.9 - - - +
175A MET* 1.3 63.6 + - - +
501A HEC 5.4 0.9 - - - -
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Residues in contact with MET 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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88A GLN* 3.5 3.6 - - - -
89A VAL* 2.9 54.3 + - + +
105A ASP* 3.6 35.0 - - - +
108A ALA* 3.7 13.2 - - + -
109A LEU* 3.7 16.6 - - + -
112A PHE* 3.8 19.7 - - + -
132A PHE* 3.6 36.1 - - + -
133A ARG 3.2 13.2 - - - +
135A ILE* 3.5 14.1 - - - +
174A GLY* 1.3 73.4 - - - +
176A TYR* 1.3 66.1 + - - +
177A ALA* 4.6 0.4 - - + -
501A HEC 5.5 0.2 - - - +
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Residues in contact with TYR 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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38A ILE* 3.5 38.1 - - + -
41A LEU* 3.9 31.8 - - + -
42A ASP* 2.6 54.2 + - + -
45A ARG* 3.0 33.3 + - - -
71A VAL* 4.4 0.4 - - + -
86A VAL* 6.0 2.5 - - + -
87A ARG 3.8 4.9 - - - +
88A GLN* 4.1 15.0 - - + -
131A TYR* 4.4 1.3 - - + -
132A PHE* 3.2 6.1 - - - -
133A ARG* 2.8 46.3 + - + +
135A ILE* 3.4 14.5 - - + +
175A MET* 1.3 76.9 - - - +
177A ALA* 1.3 60.6 + - - +
178A VAL* 5.4 0.2 - - - -
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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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85A GLN 3.7 0.9 - - - +
86A VAL* 3.4 3.5 - - - +
87A ARG* 2.8 44.6 + - + +
89A VAL* 4.1 17.3 - - + -
105A ASP* 4.8 3.1 - - - +
131A TYR 3.4 4.3 - - - -
132A PHE* 3.8 24.2 - - + -
175A MET* 4.6 0.9 - - + -
176A TYR* 1.3 74.9 - - - +
178A VAL* 1.3 63.7 + - - +
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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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34A VAL* 3.9 28.0 - - + -
38A ILE* 3.5 39.0 - - + -
84A TRP* 4.1 24.5 - - + -
85A GLN 3.1 9.0 - - - +
86A VAL* 4.1 11.9 - - + -
129A VAL 3.7 0.2 - - - +
130A HIS* 3.1 6.6 - - - +
131A TYR* 2.8 40.0 + - + +
132A PHE* 5.3 0.5 - - - -
176A TYR 5.4 0.2 - - - -
177A ALA* 1.3 80.1 - - - +
179A THR* 1.3 69.5 + - - +
180A ILE* 4.7 2.0 - - + +
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Residues in contact with THR 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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84A TRP* 3.4 5.2 - - - +
85A GLN* 2.8 62.6 + - - +
127A GLU* 4.4 7.2 - - + +
129A VAL 3.3 4.9 - - - +
130A HIS* 2.9 37.2 + - + +
178A VAL* 1.3 76.1 - - - +
180A ILE* 1.3 75.3 + - - +
181A PRO* 3.3 13.1 - - + +
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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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26A ALA* 3.9 24.9 - - + +
30A GLU* 3.7 42.4 - - + +
31A LEU* 4.0 16.6 - - + -
34A VAL* 4.0 18.8 - - + -
84A TRP* 4.1 14.8 - - + +
128A GLY* 3.5 0.9 - - - -
129A VAL* 2.7 42.6 + - + +
178A VAL* 4.9 2.2 - - + -
179A THR* 1.3 74.5 - - - +
181A PRO* 1.3 69.6 - - + +
184A GLN* 3.8 16.8 - - - +
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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
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26A ALA 5.7 0.7 + - - -
83A GLY 3.4 23.3 - - - +
84A TRP* 4.4 0.9 - - - -
85A GLN* 4.3 16.8 - - - +
127A GLU 3.5 8.7 - - - +
179A THR* 3.3 16.3 - - + +
180A ILE* 1.3 86.6 - - + +
182A GLN* 1.3 62.4 + - - +
183A ILE 3.7 17.0 - - - +
184A GLN* 2.8 39.4 + - + +
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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