Contacts of the strand formed by residues 165 - 172 (chain A) in PDB entry 4OI9
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 PHE 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.3 10.7 - - + +
97A LEU* 4.0 7.6 - - + -
107A PHE* 4.0 19.3 - + - -
109A LEU* 3.9 34.5 - - + -
127A LEU 3.3 14.6 - - - +
128A ARG* 3.5 39.0 - - + -
133A LEU* 3.9 9.2 - - + -
154A VAL* 4.7 2.7 - - + -
160A ASP* 4.4 7.9 - - - -
163A ALA* 3.9 13.7 - - + -
164A ASN* 1.3 75.0 - - - +
166A SER* 1.3 62.0 + - - +
187A PRO* 3.5 1.3 - - - +
188A ARG 2.7 46.7 + - - +
190A LEU* 3.5 36.3 - - + -
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Residues in contact with SER 166 (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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94A LEU* 3.8 7.4 - - - +
109A LEU* 5.8 1.1 - - - +
126A LEU* 3.7 4.2 - - - +
127A LEU* 2.9 48.6 + - - +
129A GLY 4.7 4.9 + - - -
164A ASN 5.4 0.5 + - - -
165A PHE* 1.3 75.0 - - - +
167A CYS* 1.3 63.9 + - - +
184A SER* 5.5 3.7 - - - -
185A SER* 3.6 21.3 - - - -
187A PRO* 4.3 12.8 - - - -
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Residues in contact with CYS 167 (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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92A VAL* 3.5 3.4 - - + +
94A LEU* 4.4 6.3 - - + +
111A CYS* 2.0 60.1 - - + -
124A LEU* 4.8 5.8 - - - -
125A THR 3.4 10.5 - - - -
126A LEU* 3.6 13.2 - - + -
150A LEU* 5.3 0.7 - - - -
166A SER* 1.3 76.1 - - - +
168A ARG* 1.3 68.0 + - - +
184A SER* 3.4 4.7 - - - -
185A SER* 2.8 39.4 + - - +
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Residues in contact with ARG 168 (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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123A THR 3.5 2.8 - - - +
124A LEU* 3.3 3.8 - - - -
125A THR* 2.7 60.0 + - - +
127A LEU* 3.7 23.7 - - + +
132A GLU* 4.5 6.9 + - - -
135A ARG* 4.2 10.5 - - - +
167A CYS* 1.3 78.5 - - - +
169A ALA* 1.3 71.8 + - - +
170A GLU* 4.4 18.6 + - - -
182A GLU* 2.9 29.3 + - - +
183A ASN 3.9 2.9 - - - +
184A SER* 3.2 22.0 - - - +
2334A EDO 4.6 2.1 + - - +
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Residues in contact with ALA 169 (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 PRO* 3.9 8.6 - - + +
92A VAL* 3.7 16.5 - - + +
113A VAL* 3.7 37.5 - - + -
122A LEU* 5.4 2.0 - - + -
123A THR 3.7 2.9 - - - -
124A LEU* 4.2 8.1 - - + -
167A CYS 4.3 0.6 - - - -
168A ARG* 1.3 74.2 - - - +
170A GLU* 1.3 60.2 + - - +
171A LEU 4.3 0.2 - - - -
182A GLU* 3.2 7.4 - - - +
183A ASN 3.1 29.4 + - - +
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Residues in contact with GLU 170 (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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121A SER 3.3 2.8 - - - +
122A LEU* 3.3 6.6 - - - +
123A THR* 2.7 47.2 + - - +
125A THR* 5.3 0.7 + - - -
135A ARG* 3.5 19.8 + - - -
168A ARG* 4.4 22.9 + - - -
169A ALA* 1.3 74.7 - - - +
171A LEU* 1.3 61.2 + - - +
172A ASP 3.9 0.2 + - - -
180A LEU* 3.8 29.5 - - + +
181A PHE 3.8 1.8 - - - +
182A GLU* 4.1 21.9 - - + +
2327A EDO 3.5 30.6 + - - +
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Residues in contact with LEU 171 (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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86A PHE* 4.0 18.4 - - + -
87A GLN 3.5 16.8 - - - +
88A ARG* 4.4 0.9 - - - -
89A PRO* 4.2 4.7 - - + +
117A GLY 3.3 35.9 - - - +
118A PRO* 3.8 6.5 - - + +
121A SER* 3.7 24.5 - - - -
122A LEU* 3.8 15.7 - - + +
170A GLU* 1.3 73.7 - - - +
172A ASP* 1.3 58.7 + - - +
173A LEU* 3.6 11.2 + - + -
179A GLY 4.0 0.2 - - - +
180A LEU* 3.4 7.6 - - - +
181A PHE* 2.7 60.8 + - + +
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Residues in contact with ASP 172 (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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121A SER* 3.0 39.1 + - - +
170A GLU 3.9 0.2 + - - -
171A LEU* 1.3 72.0 - - - +
173A LEU* 1.3 59.4 + - - +
174A ARG* 2.4 60.1 + - - +
175A PRO* 3.4 11.6 - - - +
180A LEU* 3.6 9.2 - - + -
2326A EDO 4.7 1.4 + - - -
2327A EDO 3.4 17.4 - - - +
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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