Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 3SRG
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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.0 1.7 - - - +
101A GLU* 3.3 24.0 - - - +
103A ILE* 4.1 14.2 - - - +
146A PHE* 3.6 6.7 - - - -
147A GLN* 2.7 60.2 + - - +
150A GLU* 3.6 13.9 - - - +
151A LYS* 1.3 81.8 - - - +
153A LEU* 1.3 62.4 + - - +
154A LEU 4.1 0.2 - - - -
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Residues in contact with LEU 153 (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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64A PHE* 4.3 0.9 - - + -
85A ILE* 3.7 37.7 - - + -
100A LEU* 3.7 28.5 - - + -
101A GLU 2.8 10.2 + - - +
102A ILE* 3.3 14.6 - - + +
103A ILE* 2.7 34.8 + - - +
129A LEU* 3.9 24.7 - - + -
144A PHE* 3.7 25.1 - - + -
145A LYS 3.5 1.1 - - - -
146A PHE* 4.0 26.0 - - + -
152A SER* 1.3 73.9 - - - +
154A LEU* 1.3 56.8 + - - +
155A HIS 3.7 1.1 + - - -
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Residues in contact with LEU 154 (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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103A ILE* 3.6 28.9 - - + +
104A GLY* 4.6 4.7 - - - -
144A PHE* 3.3 1.3 - - - -
145A LYS* 2.9 48.0 + - + +
147A GLN* 3.9 31.6 + - - +
152A SER 4.1 0.8 - - - -
153A LEU* 1.3 70.4 - - - +
155A HIS* 1.3 74.9 + - - +
156A LEU* 3.4 18.4 + - + +
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Residues in contact with HIS 155 (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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102A ILE* 4.8 2.0 - - + -
103A ILE 3.0 16.6 + - - +
104A GLY* 4.9 5.1 - - - -
106A THR* 2.6 50.0 + - - +
107A LEU* 3.8 17.4 - - + +
142A GLU* 2.7 29.5 + - + -
143A VAL 3.6 11.9 - - - -
144A PHE* 3.6 29.5 - + + -
153A LEU 3.7 2.2 + - - -
154A LEU* 1.3 80.0 - - - +
156A LEU* 1.3 62.7 + - - +
157A LYS 3.3 19.6 + - - -
158A THR* 3.3 19.5 - - - -
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Residues in contact with LEU 156 (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 THR* 4.2 10.6 + - - +
128A TYR* 3.6 36.3 - - + -
143A VAL* 2.8 20.6 + - + +
144A PHE 4.4 1.1 - - - -
145A LYS* 4.0 16.6 - - + +
154A LEU* 3.8 30.3 - - + +
155A HIS* 1.3 83.6 - - - +
157A LYS* 1.4 65.1 + - + +
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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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106A THR* 5.8 0.4 - - - -
141A VAL 3.8 0.9 - - - +
142A GLU* 3.4 1.6 - - - -
143A VAL* 2.7 45.8 + - + +
155A HIS* 3.3 12.7 + - - -
156A LEU* 1.4 82.8 - - + +
158A THR* 1.3 79.5 + - - +
159A ILE* 4.2 14.4 - - + +
176A GLU* 3.4 30.1 - - + +
208A TYR* 4.9 8.1 + - - -
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Residues in contact with THR 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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106A THR 4.1 6.7 + - - -
107A LEU* 4.6 1.6 - - - +
140A THR* 3.8 17.7 - - + -
142A GLU* 2.6 27.8 + - - +
155A HIS* 3.3 12.8 - - - -
157A LYS* 1.3 89.8 + - - +
159A ILE* 1.4 62.0 + - - +
160A ARG* 3.8 37.1 + - - +
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Residues in contact with ILE 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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140A THR* 3.0 9.2 - - - -
141A VAL* 2.7 43.8 + - + +
143A VAL* 3.8 25.4 - - + -
157A LYS* 4.2 17.7 - - + +
158A THR* 1.4 73.6 - - - +
160A ARG* 1.3 62.9 + - - +
164A LEU* 4.1 12.8 - - + +
176A GLU* 4.0 15.9 - - + +
178A PHE* 3.9 18.8 - - + -
208A TYR* 3.4 54.5 - - + +
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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