Contacts of the strand formed by residues 146 - 156 (chain C) in PDB entry 4STD
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 GLY 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.8 4.9 - - - +
47C ARG 3.1 16.4 - - - -
48C ILE* 4.4 1.8 - - - -
133C HIS* 3.7 0.5 - - - -
134C TRP* 3.2 23.8 + - - +
144C PHE* 3.1 31.0 - - - -
145C ALA* 1.3 79.4 - - - +
147C LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TRP* 3.8 23.3 - - + +
30C TYR* 4.7 1.8 - - - +
47C ARG 3.0 6.5 + - - +
48C ILE* 3.9 19.1 - - + -
49C ASP 3.1 25.1 + - - +
50C TYR* 3.9 20.9 - - + +
66C PHE* 4.7 3.8 - - + -
131C ASN* 4.2 1.6 - - - +
132C LEU 3.3 7.4 - - - -
133C HIS* 3.4 18.8 - - + +
134C TRP* 3.6 6.5 - - - -
144C PHE* 3.5 11.4 - - + -
146C GLY* 1.3 78.1 - - - +
148C LYS* 1.3 61.1 + - - +
149C PRO* 3.9 9.4 - - + -
175C BFS 3.7 32.8 - - - +
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Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 3.0 46.0 + - + +
51C ARG* 4.0 19.2 - - - +
52C SER* 5.4 2.2 - - - +
130C ALA 3.8 1.2 - - - +
131C ASN* 4.8 0.4 - - - -
132C LEU* 2.7 52.3 + - + +
134C TRP* 3.9 15.9 - - + -
147C LEU* 1.3 75.4 - - - +
149C PRO* 1.3 66.0 - - - +
150C ASP* 3.6 5.2 + - + +
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Residues in contact with PRO 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP 3.2 16.0 - - - +
50C TYR* 4.0 22.4 - - + -
52C SER* 2.7 26.5 + - - -
53C PHE* 4.8 11.2 - - + +
131C ASN* 3.5 25.3 - - - +
147C LEU* 3.8 14.4 - - + +
148C LYS* 1.3 88.7 - - - +
150C ASP* 1.3 52.4 + - - +
151C ILE* 3.6 6.9 - - + +
175C BFS 3.7 24.7 - - + +
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Residues in contact with ASP 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER* 3.7 12.2 - - - -
129C SER* 3.2 2.8 - - - -
130C ALA* 2.9 34.4 + - + +
131C ASN* 4.3 0.6 - - - +
148C LYS* 3.6 4.0 + - + +
149C PRO* 1.3 69.7 - - - +
151C ILE* 1.3 63.4 + - - +
152C ARG* 3.0 50.3 + - - +
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Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER* 3.5 20.1 + - - +
53C PHE* 3.7 26.9 - - + -
127C ALA* 3.8 22.4 - - + -
128C HIS 4.0 4.9 - - - +
129C SER* 3.7 14.4 - - - -
149C PRO* 4.6 8.5 - - + +
150C ASP* 1.3 72.0 + - - +
152C ARG* 1.3 63.7 + - - +
153C TRP* 4.1 10.5 - - - +
158C PHE* 3.7 35.4 - - + -
175C BFS 3.9 19.1 - - + -
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Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 2.8 42.6 + - - -
31A ASP* 4.0 22.4 + - - +
32A SER* 3.9 21.4 - - - +
37A ARG* 4.5 1.2 - - - +
82A ARG* 3.4 33.6 + - - +
118A MET* 5.5 0.7 - - - +
128C HIS 3.0 9.7 + - - +
129C SER* 4.5 4.2 - - - +
130C ALA* 3.4 20.2 - - - +
150C ASP* 3.0 53.8 + - - +
151C ILE* 1.3 74.1 - - - +
153C TRP* 1.3 73.6 + - + +
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Residues in contact with TRP 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 3.6 33.7 - - + +
83A THR* 3.0 39.5 + - - +
109A PRO* 3.8 25.1 - - + -
111A GLN* 3.2 55.4 - - + -
113A TYR* 4.0 7.0 - - - +
118A MET* 5.4 1.6 - - - -
126A HIS* 5.3 1.6 - + - -
127C ALA* 3.8 1.4 - - - -
128C HIS* 2.9 76.6 + + + +
151C ILE* 3.5 7.9 - - - +
152C ARG* 1.3 95.2 - - + +
154C GLY* 1.3 67.1 + - - +
155C GLU* 4.4 2.7 - - + -
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Residues in contact with GLY 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 3.0 18.7 + - - -
113A TYR* 3.8 3.7 + - - -
126C HIS 3.1 12.6 - - - -
127C ALA* 4.2 2.7 - - - -
128C HIS* 3.9 0.7 - - - -
151C ILE* 5.8 0.2 - - - -
153C TRP* 1.3 83.4 - - - +
155C GLU* 1.3 63.4 + - - -
156C PHE 4.1 4.4 + - - +
158C PHE* 4.7 10.5 - - - -
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 4.2 3.8 + - - -
109A PRO* 5.0 0.6 - - - +
111A GLN* 3.6 18.8 - - - +
124A LYS* 2.8 28.4 + - + +
126A HIS* 3.0 28.6 + - + +
155A GLU* 5.4 0.2 - - - +
156A PHE* 3.8 5.4 - - - -
107C ARG* 3.8 20.5 + - - -
125C GLY* 3.6 0.9 - - - -
126C HIS* 2.7 40.4 + - + +
128C HIS* 3.8 16.9 + - + -
153C TRP* 4.6 0.9 - - + -
154C GLY* 1.3 72.7 - - - -
156C PHE* 1.3 89.7 + - + +
158C PHE 4.2 1.2 + - - -
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Residues in contact with PHE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 4.4 2.6 + - - -
121A VAL* 6.3 0.8 - - - +
124A LYS* 3.7 23.5 - - - +
156A PHE* 4.6 9.0 - + - -
155B GLU* 3.7 9.4 - - - -
156B PHE* 4.7 5.6 - + - -
124C LYS* 3.4 34.3 - - + +
126C HIS* 3.3 42.8 - + - -
154C GLY 4.1 4.7 + - - +
155C GLU* 1.3 90.5 - - - +
157C ASP* 1.3 71.0 + - - +
158C PHE 4.0 1.2 + - - -
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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