Contacts of the strand formed by residues 104 - 111 (chain A) in PDB entry 4O65
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.4 17.9 - - + -
42A VAL* 3.6 30.1 - - + -
98A SER* 5.0 1.1 - - - +
100A VAL* 3.6 29.6 - - + -
102A GLN* 4.0 9.0 - - + +
103A ASP* 1.3 81.6 - - - +
105A ASN* 1.3 66.4 + - - +
134A THR* 3.3 5.5 - - - +
135A ILE* 2.7 47.6 + - + +
163A ILE* 3.9 26.2 - - + -
164A ALA 5.3 2.7 - - - +
165A SER* 5.9 0.7 - - - +
166A VAL* 5.0 4.5 - - + -
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Residues in contact with ASN 105 (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 LEU* 1.3 77.4 - - - +
106A ALA* 1.3 62.8 + - - +
132A VAL* 3.7 19.4 - - + +
133A PHE 3.3 4.5 - - - +
134A THR* 3.7 16.6 + - - +
163A ILE* 3.7 5.4 - - - +
164A ALA* 2.8 41.7 + - + +
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Residues in contact with ALA 106 (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 LEU* 5.7 0.2 - - + -
105A ASN* 1.3 77.2 - - - +
107A TRP* 1.3 67.4 + - - +
132A VAL* 3.3 5.2 - - - +
133A PHE* 2.8 41.3 + - + -
135A ILE* 3.7 29.2 - - + -
161A LEU* 3.8 12.6 - - + -
162A ASN 3.1 15.9 - - - +
163A ILE* 4.3 4.7 - - + -
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Residues in contact with TRP 107 (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 ALA* 1.3 77.5 - - - +
108A ILE* 1.3 67.1 + - - +
109A SER* 5.4 4.3 - - - -
126A ARG* 6.2 1.3 - - - +
131A ASN 3.2 25.8 - - - +
132A VAL* 4.2 17.5 - - + -
133A PHE* 3.9 7.6 - - - -
160A GLN 4.0 0.2 - - - +
161A LEU* 3.6 4.5 - - - +
162A ASN* 2.8 70.0 + - + +
163A ILE 4.9 1.1 - - - -
164A ALA* 3.8 35.7 - - + -
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Residues in contact with ILE 108 (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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96A LEU* 4.3 15.7 - - + -
107A TRP* 1.3 81.1 - - - +
109A SER* 1.3 65.4 + - - +
123A PHE* 4.8 0.2 - - - -
126A ARG* 3.0 45.1 + - + +
127A ASP 5.3 4.7 - - - +
128A PRO 5.4 1.1 - - - +
133A PHE* 4.0 18.6 - - + -
143A TYR* 3.6 42.2 - - + -
145A LEU* 3.7 23.3 - - + -
159A THR* 3.9 17.9 - - + -
160A GLN 3.4 10.3 - - - +
161A LEU* 4.7 3.6 - - + -
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Residues in contact with SER 109 (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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107A TRP* 5.4 5.4 - - - -
108A ILE* 1.3 76.6 - - - +
110A LEU* 1.3 64.1 + - - +
123A PHE* 3.8 15.3 - - - -
126A ARG* 4.1 9.0 - - - -
145A LEU* 3.8 11.0 - - - +
159A THR* 3.8 1.0 - - - -
160A GLN* 2.8 53.5 + - - +
162A ASN* 4.6 4.0 + - - -
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Residues in contact with LEU 110 (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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49A PHE* 4.5 1.8 - - + -
90A LEU* 4.5 7.9 - - + -
92A VAL* 4.2 23.6 - - + -
109A SER* 1.3 80.6 + - - +
111A PHE* 1.3 62.6 + - - +
112A THR 3.9 21.3 + - - +
121A TRP* 4.3 19.3 - - + -
123A PHE* 3.9 5.7 - - + -
145A LEU* 4.8 3.8 - - + -
147A LEU* 3.9 37.5 - - + -
157A ALA* 4.2 16.2 - - + -
158A HIS 3.5 20.6 - - - +
159A THR* 4.4 3.8 - - - +
160A GLN* 4.8 0.9 + - - -
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Residues in contact with PHE 111 (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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109A SER 4.1 1.0 - - - -
110A LEU* 1.3 72.2 - - - +
112A THR* 1.4 88.3 + - + +
156A HIS 3.7 0.4 - - - +
157A ALA* 3.3 2.6 - - - +
158A HIS* 2.8 61.5 + + + +
160A GLN* 3.3 27.0 - - + +
170A LEU* 3.9 32.1 - - + -
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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