Contacts of the strand formed by residues 105 - 113 (chain A) in PDB entry 4TZQ
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.5 2.0 - - + -
96A ALA* 3.2 30.1 - - + +
99A ALA* 3.8 16.6 + - + -
100A THR* 4.0 9.9 - - + -
103A GLY 3.4 0.6 - - - -
104A PHE* 1.3 77.5 - - - +
106A LYS* 1.3 60.4 + - - +
107A GLU 3.4 28.3 - - - +
108A VAL* 4.2 7.2 - - + +
129A PHE* 3.4 34.6 - - + +
131A TYR* 2.5 32.5 + - - +
199A LEU* 4.3 11.7 - - + -
200A GLU 3.9 5.6 - - - +
202A THR* 4.1 2.5 - - - -
211A ILE* 4.4 12.3 - - + -
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Residues in contact with LYS 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 PHE 3.9 0.8 + - - -
105A LEU* 1.3 71.7 - - - +
107A GLU* 1.3 65.3 + - + +
128A LYS* 3.5 2.4 - - - +
129A PHE* 2.8 31.4 + - - +
142A SER* 3.3 9.6 - - - +
143A THR 3.1 23.4 + - - -
144A ASP* 5.2 1.6 - - - +
150A ASP* 2.8 29.4 + - - +
152A HIS* 4.1 14.4 - - + -
200A GLU* 2.9 42.9 + - + +
201A TYR 3.8 20.6 + - - +
202A THR* 3.8 18.1 - - + +
203A ASN* 4.3 11.1 + - - +
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Residues in contact with GLU 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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105A LEU* 3.4 6.7 - - - +
106A LYS* 1.3 88.5 - - + +
108A VAL* 1.3 62.6 + - - +
109A SER* 2.8 19.8 + - - +
126A SER* 3.7 3.3 - - - -
127A MET 3.3 12.3 - - - +
128A LYS* 3.7 27.5 + - + +
129A PHE* 4.3 1.6 - - - -
199A LEU* 3.1 7.6 - - - +
200A GLU* 3.0 32.8 + - + +
220A PHE* 3.4 26.4 - - + -
221A TYR* 2.6 30.3 + - - -
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Residues in contact with VAL 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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46A ILE* 4.1 13.0 - - + -
50A PHE* 3.7 19.1 - - + -
93A LEU* 4.8 7.6 - - + -
96A ALA* 4.3 17.0 - - + -
105A LEU* 4.3 11.2 - - + -
107A GLU* 1.3 74.7 - - - +
109A SER* 1.3 64.9 + - - +
127A MET* 3.0 32.1 + - + +
129A PHE* 3.8 24.8 - - + -
197A PHE* 4.4 17.3 - - + -
198A ARG 3.9 3.6 - - - +
199A LEU* 4.2 8.5 - - + -
214A PHE* 4.9 8.1 - - + -
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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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50A PHE* 4.2 1.8 - - - -
107A GLU* 2.8 27.6 + - - +
108A VAL* 1.3 82.7 + - - +
110A LEU* 1.3 60.6 + - - +
111A VAL* 3.7 2.8 + - - +
124A VAL* 4.0 13.7 - - - -
125A PHE 3.3 10.8 - - - -
126A SER* 3.2 12.6 - - - -
197A PHE* 3.2 10.1 - - - -
198A ARG 2.9 39.2 + - - -
221A TYR* 4.2 7.9 - - - -
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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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50A PHE* 3.7 12.3 - - + -
53A VAL* 4.2 16.2 - - + -
54A LEU* 4.0 17.9 - - + -
59A ILE* 3.7 29.2 - - + -
109A SER* 1.3 69.4 - - - +
111A VAL* 1.3 62.1 + - - +
112A ILE* 4.0 11.8 + - + +
123A GLU 3.9 0.9 - - - +
124A VAL* 3.5 6.2 - - - +
125A PHE* 3.1 33.9 + - + +
195A ALA* 4.3 7.9 - - + -
196A ASN* 3.4 24.9 - - - +
197A PHE* 3.6 35.0 - - + -
496B ILE* 5.6 2.2 - - + -
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Residues in contact with VAL 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* 4.0 7.4 - - - +
110A LEU* 1.3 76.8 - - - +
112A ILE* 1.3 62.5 + - - +
113A THR* 4.1 3.6 - - + -
121A ALA* 3.7 24.0 - - + -
123A GLU 3.9 2.0 - - - -
124A VAL* 4.5 2.7 - - + -
194A THR 3.5 2.3 - - - +
195A ALA* 3.3 2.6 - - - -
196A ASN* 2.6 35.8 + - - +
198A ARG* 3.6 60.4 + - + +
221A TYR* 3.8 26.5 - - + -
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Residues in contact with ILE 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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59A ILE* 3.9 23.8 - - + -
110A LEU* 4.7 10.5 - - + +
111A VAL* 1.3 78.0 - - - +
113A THR* 1.3 59.7 + - - +
121A ALA* 3.5 3.5 - - - -
122A ILE* 2.7 37.0 + - + -
123A GLU* 2.9 50.0 + - + +
125A PHE* 4.8 3.1 - - + -
189A LEU* 4.3 18.8 - - + -
193A PHE* 3.8 34.1 - - + -
194A THR 3.4 2.9 - - - +
195A ALA* 4.2 10.8 - - + -
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Residues in contact with THR 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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111A VAL* 4.1 4.9 - - + -
112A ILE* 1.3 79.2 - - - +
114A ASN* 1.3 60.1 + - - +
115A ASN 2.6 25.8 + - - -
116A GLU* 4.4 1.0 - - - -
118A ASP* 3.8 14.3 - - - +
120A GLU 3.6 19.3 - - - +
121A ALA* 3.9 6.3 - - - -
122A ILE* 3.5 12.3 - - - +
193A PHE* 3.3 8.7 - - - +
194A THR* 2.8 39.4 + - - +
198A ARG* 3.7 26.2 + - - +
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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