Contacts of the strand formed by residues 109 - 116 (chain A) in PDB entry 1Z78
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 THR 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A SER* 3.8 2.8 + - - -
104A ASN* 2.9 37.6 + - - +
107A ALA* 3.7 21.4 - - + +
108A GLY* 1.3 84.6 - - - +
110A LEU* 1.3 60.7 + - - +
111A ASP* 2.8 24.6 + - - -
124A SER* 3.9 16.7 + - - +
125A VAL 3.3 15.7 - - - +
126A GLU* 4.2 14.1 - - + +
127A GLU 5.0 0.2 - - - +
128A ALA 3.5 11.1 + - - +
130A LEU* 5.4 0.3 - - - +
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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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86A LEU* 4.1 8.7 - - + -
101A VAL* 4.0 19.7 - - + -
102A VAL 3.4 12.3 - - - +
103A SER* 4.0 7.0 - - - -
109A THR* 1.3 73.7 - - - +
111A ASP* 1.3 62.0 + - - +
112A LEU* 3.9 5.2 + - + +
124A SER* 3.8 0.5 - - - -
125A VAL* 2.8 38.3 + - + +
128A ALA* 4.1 2.9 - - + +
130A LEU* 3.8 22.7 - - + -
138A ILE* 4.1 8.3 - - + -
140A LEU* 4.0 24.0 - - + -
149A LEU* 3.8 43.3 - - + -
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Residues in contact with ASP 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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100A SER 3.6 1.0 - - - +
101A VAL* 3.4 4.9 - - - -
102A VAL* 2.7 52.8 + - + +
104A ASN* 3.0 29.6 + - - +
109A THR* 2.8 18.4 + - - -
110A LEU* 1.3 72.3 - - - +
112A LEU* 1.3 62.7 + - - +
113A SER* 4.1 3.3 + - - +
122A VAL* 4.4 14.4 - - + +
123A VAL 3.6 3.8 - - - +
124A SER* 2.7 29.2 + - - -
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Residues in contact with LEU 112 (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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99A PHE* 5.0 6.5 - - + -
100A SER 3.4 3.1 - - - +
101A VAL* 3.8 32.3 - - + -
110A LEU* 4.4 10.1 - - + +
111A ASP* 1.3 79.2 - - - +
113A SER* 1.3 60.9 + - - +
114A LEU* 4.1 7.8 - - + +
121A HIS 3.8 1.2 - - - +
122A VAL* 3.5 1.4 - - - -
123A VAL* 2.9 38.2 + - + +
125A VAL* 4.3 13.9 - - + -
140A LEU* 4.0 18.8 - - + -
142A VAL* 5.0 4.3 - - + -
147A ALA* 3.8 28.9 - - + -
159A ALA* 5.5 1.6 - - + -
161A LEU* 4.1 21.7 - - + +
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Residues in contact with SER 113 (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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97A GLN* 5.9 1.3 - - - -
99A PHE* 3.1 11.4 - - - -
100A SER* 2.9 48.1 + - - -
102A VAL* 5.8 1.6 - - - +
111A ASP* 5.1 3.1 - - - +
112A LEU* 1.3 73.2 + - - +
114A LEU* 1.3 63.2 - - - +
115A THR* 4.3 1.1 - - - -
120A GLN* 4.8 11.0 + - - -
121A HIS 3.3 8.1 - - - -
122A VAL* 3.4 25.6 - - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A VAL 3.5 4.3 - - - -
99A PHE* 3.6 23.8 - - + -
112A LEU* 4.1 3.4 - - + +
113A SER* 1.3 85.3 - - - +
115A THR* 1.3 62.2 + - - +
116A VAL* 3.9 0.9 - - + -
119A LYS 3.5 1.7 - - - +
120A GLN* 4.6 0.2 - - - -
121A HIS* 2.9 40.5 + - + +
123A VAL* 6.4 0.4 - - + -
161A LEU* 3.9 43.3 - - + -
163A VAL* 3.8 27.6 - - + +
165A ILE* 4.1 12.8 - - + -
168A VAL* 3.5 24.0 - - + -
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Residues in contact with THR 115 (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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91A ARG* 6.5 0.9 - - - -
97A GLN 3.2 25.3 + - - +
98A VAL* 2.8 29.7 + - + +
113A SER* 5.6 0.7 - - - -
114A LEU* 1.3 71.2 - - - +
116A VAL* 1.3 62.2 + - - +
117A GLN* 3.6 11.1 + - - +
118A GLY* 4.2 6.5 - - - +
119A LYS 3.0 22.7 - - - +
120A GLN* 3.6 22.0 + - + +
168A VAL* 4.8 3.5 - - - +
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Residues in contact with VAL 116 (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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114A LEU 3.9 1.7 + - - +
115A THR* 1.3 76.4 - - - +
117A GLN* 1.3 70.0 + - + +
119A LYS* 3.0 25.8 + - - +
121A HIS* 4.8 9.4 + - + +
163A VAL* 3.7 31.2 - - + -
167A SER* 3.4 33.7 - - - +
168A VAL* 3.9 16.4 - - + -
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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