Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 3COG
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLN* 2.2 39.4 + - - +
108A ILE* 3.8 25.1 - - + -
147A ILE* 3.7 4.2 - - + -
148A THR* 2.8 29.9 + - - +
149A PRO 4.4 1.2 - - - +
150A GLU* 1.3 75.3 - - - +
152A LYS* 1.3 70.2 + - - +
153A LEU 4.2 2.7 - - - +
154A VAL* 4.1 15.0 - - + -
182A ILE* 3.2 34.8 - - + +
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Residues in contact with LYS 152 (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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101A LEU* 3.7 21.5 - - + -
102A LYS* 5.0 7.9 - - - +
105A ASP* 3.6 26.9 - - + +
106A GLN 3.0 6.6 + - - +
149A PRO 3.7 20.6 - - - -
150A GLU* 3.2 18.9 + - - +
151A THR* 1.3 77.0 - - - +
153A LEU* 1.3 61.4 + - - +
181A ASP* 3.9 33.2 + - - +
182A ILE* 3.6 7.3 - - - -
183A ILE* 2.9 31.1 + - + +
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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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97A ILE* 4.2 20.9 - - + +
98A THR* 4.6 10.1 - - - +
101A LEU* 3.9 31.0 - - + -
106A GLN 3.5 2.7 + - - +
107A ILE* 3.4 24.7 - - + -
108A ILE* 2.9 26.3 + - - +
121A PHE* 4.9 1.1 - - + -
151A THR* 3.8 1.8 - - - +
152A LYS* 1.3 80.9 - - - +
154A VAL* 1.3 70.1 + - - +
155A TRP* 4.5 11.4 - - + +
182A ILE* 3.9 0.2 - - - +
183A ILE* 3.5 25.4 - - + +
185A VAL* 3.4 31.2 - - + -
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Residues in contact with VAL 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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108A ILE* 3.3 16.4 - - + +
137A CYS* 4.9 0.4 - - - -
143A LEU* 4.0 24.9 - - + -
147A ILE* 5.3 1.1 - - + -
151A THR* 4.1 12.3 - - + -
153A LEU* 1.3 77.3 - - - +
155A TRP* 1.3 56.9 + - - +
156A ILE* 4.1 13.7 - - + -
176A VAL* 3.7 17.9 - - + -
182A ILE* 3.6 22.0 - - + -
183A ILE 2.8 11.4 + - - +
184A LEU* 3.5 20.2 - - + +
185A VAL* 2.8 33.1 + - - +
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Residues in contact with TRP 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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94A THR* 3.3 42.8 - - + -
97A ILE* 3.6 28.0 - - + -
107A ILE* 4.8 3.8 - - + -
108A ILE 2.8 14.1 + - - +
109A CYS* 4.1 15.7 - - + -
110A MET* 2.9 27.5 + - - +
113A VAL* 4.5 6.6 - - + +
117A THR* 3.7 18.7 - - + +
121A PHE* 3.9 27.4 - + + -
153A LEU* 4.5 9.2 - - + -
154A VAL* 1.3 70.7 - - - +
156A ILE* 1.3 70.4 + - - +
157A GLU* 4.8 1.4 - - - +
185A VAL* 3.6 35.7 - - + -
187A ASP* 4.1 17.7 + - + +
207A MET* 3.9 21.8 - - + -
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Residues in contact with ILE 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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110A MET* 4.0 6.1 - - + -
137A CYS* 4.2 23.8 - - + -
154A VAL* 4.1 20.2 - - + -
155A TRP* 1.3 84.4 - - - +
157A GLU* 1.3 60.4 - - - +
158A THR* 4.6 3.4 - - + -
167A ILE* 3.4 34.8 - - + -
169A ILE* 4.3 10.5 - - + -
172A CYS* 5.0 6.3 - - + -
184A LEU* 4.5 10.5 - - + -
185A VAL 2.9 17.3 + - - +
186A VAL* 3.3 22.7 - - + -
187A ASP* 2.8 32.9 + - - +
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Residues in contact with GLU 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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110A MET* 4.2 6.7 - - - +
113A VAL* 3.3 21.3 - - + +
114A TYR* 2.7 35.1 + - - +
117A THR* 4.4 2.8 + - - -
155A TRP* 4.8 2.1 + - - +
156A ILE* 1.3 74.1 - - - +
158A THR* 1.3 66.9 + - - +
159A PRO 4.1 7.2 - - - +
160A THR* 3.5 12.2 - - + +
161A ASN* 2.9 32.6 + - - +
167A ILE* 3.2 19.1 - - - +
187A ASP* 3.7 32.4 - - + +
500A PLP 3.9 13.4 + - + +
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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