Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 1SGT
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.7 34.9 - - + +
19A GLY* 4.8 6.5 - - - +
20A THR* 3.2 26.5 - - - +
21A ARG* 3.9 16.2 - - + +
139A ALA* 3.1 5.9 - - - +
140A GLY 2.9 37.4 + - - +
142A GLY 5.0 0.2 - - - +
144A ASN* 4.1 12.1 - - + +
152A GLN* 4.0 27.4 - - + +
154A TYR* 3.8 11.7 - - + +
155A LEU* 1.4 80.0 - - - +
157A LYS* 1.3 62.8 - - - +
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Residues in contact with LYS 157 (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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16A VAL* 4.2 2.2 - - - -
19A GLY* 3.2 4.5 - - - -
20A THR* 2.7 64.9 + - + +
21A ARG 3.8 9.0 - - - -
22A ALA* 4.1 5.4 - - + -
26A GLU* 2.7 30.4 + - - +
27A PHE* 3.7 33.6 - - + -
137A THR* 4.5 4.7 - - + -
138A VAL 3.3 12.1 - - - +
139A ALA* 4.3 1.3 - - + +
156A LEU* 1.3 75.6 - - - +
158A ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 158 (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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16A VAL* 3.6 19.7 - - + +
18A GLY 4.5 1.6 - - - +
19A GLY* 4.3 5.4 - - - -
20A THR* 6.0 0.2 - - - -
137A THR* 3.3 6.4 - - - +
138A VAL* 3.0 38.1 + - + +
157A LYS* 1.3 78.8 - - - +
159A ASN* 1.3 62.9 + - - +
188A VAL* 3.6 27.6 - - + -
189A ASP 5.5 0.2 - - - +
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Residues in contact with ASN 159 (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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135A THR* 3.5 21.8 - - + +
136A PHE 3.1 4.9 + - - -
137A THR* 2.9 29.9 + - - +
158A ALA* 1.3 72.6 + - - +
160A VAL* 1.3 68.0 - - - +
185A TYR* 3.6 16.4 + - - +
188A VAL* 3.7 10.6 - - - +
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Residues in contact with VAL 160 (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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135A THR* 4.3 2.2 - - - -
136A PHE* 2.8 36.7 + - - +
138A VAL* 4.0 32.3 - - + -
159A ASN* 1.3 79.1 - - - +
161A PRO* 1.3 69.9 - - + +
183A ALA* 3.7 19.3 - - + +
184A GLY* 3.9 15.7 - - - +
185A TYR* 4.6 0.9 - - + -
188A VAL* 3.8 33.7 - - + +
189A ASP* 4.5 6.7 - - - +
199A MET* 4.3 3.8 - - - -
228A TYR* 4.3 5.4 - - - +
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Residues in contact with PRO 161 (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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134A GLY 3.5 8.1 - - - +
135A THR* 4.2 12.8 - - + +
160A VAL* 1.3 87.9 - - + +
162A PHE* 1.3 67.3 + - - +
183A ALA* 3.1 3.0 - - - -
184A GLY 2.9 41.7 + - - +
185A TYR* 3.4 40.6 - - + +
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Residues in contact with PHE 162 (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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132A ASN* 3.5 22.4 - - + -
133A GLN* 3.8 12.1 - - + -
134A GLY 2.8 26.8 + - - +
136A PHE* 3.7 17.0 - + + -
161A PRO* 1.3 77.2 - - - +
163A VAL* 1.3 72.9 - - - +
164A SER* 3.7 33.0 - - - -
165A ASP* 4.8 4.5 - - - -
181A ILE* 3.7 32.1 - - + -
182A CYS 3.7 1.8 - - - -
184A GLY 5.0 0.2 - - - +
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Residues in contact with VAL 163 (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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162A PHE* 1.3 86.0 - - - +
164A SER* 1.3 76.6 + - - +
165A ASP* 3.7 0.9 + - - +
167A ALA* 3.9 12.1 - - + -
168A CYS* 3.8 15.5 - - + +
182A CYS* 2.9 31.1 + - + +
183A ALA* 4.1 2.5 - - - -
184A GLY 3.5 33.9 - - - +
185A PRO* 3.7 22.9 - - + -
225A PRO* 4.0 18.8 - - + -
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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