Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 4TLG
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 ALA 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A CYS* 4.4 1.6 - - - -
97A PRO* 3.3 19.3 - - + +
131A LEU* 4.0 26.7 - - + -
135A CYS* 4.9 1.1 - - - -
148A MET* 1.3 74.8 - - - +
150A LEU* 1.3 63.0 + - - +
151A MET* 5.4 0.2 - - + -
185A THR 2.9 8.0 + - - +
186A LEU* 3.3 12.5 - - + +
187A LYS* 2.8 28.1 + - - -
513A EDO 3.9 17.9 + - - +
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Residues in contact with LEU 150 (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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92A ASP* 3.9 24.2 - - + +
96A CYS* 4.6 1.0 - - + +
97A PRO 2.9 10.4 + - - +
98A VAL* 3.3 11.5 - - + +
99A TYR* 2.9 25.3 + - - +
149A ALA* 1.3 73.7 - - - +
151A MET* 1.3 63.2 + - - +
152A VAL* 5.1 0.7 - - + -
187A LYS* 4.7 8.7 - - + -
188A ASN* 3.6 42.0 - - + +
190A ILE* 3.8 17.9 - - + -
231A PHE* 4.0 16.4 - - + -
232A ILE* 3.7 35.9 - - + -
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Residues in contact with MET 151 (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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99A TYR* 3.4 28.0 - - + -
101A ASN* 3.7 23.8 - - + +
127A VAL* 6.3 0.7 - - - -
131A LEU* 5.0 6.1 - - + -
149A ALA* 4.1 0.8 + - + -
150A LEU* 1.3 76.1 - - - +
152A VAL* 1.3 60.6 + - - +
153A PHE* 3.1 40.6 - - + -
174A PHE* 6.1 7.0 - - + -
178A LEU* 6.0 2.2 - - - -
186A LEU* 3.6 39.0 - - + -
188A ASN 3.1 14.7 + - - +
189A LEU* 3.5 0.9 - - - -
190A ILE* 2.9 27.9 + - - +
513A EDO 5.2 2.5 - - - -
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Residues in contact with VAL 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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98A VAL* 4.2 15.3 - - + -
99A TYR 2.9 7.2 + - - +
100A PHE* 3.6 36.2 - - + +
101A ASN* 2.7 34.1 + - - +
150A LEU* 5.1 1.6 - - + -
151A MET* 1.3 76.2 - - - +
153A PHE* 1.3 59.6 + - - +
154A ASP* 3.9 0.8 + - - +
190A ILE* 3.4 17.7 - - + +
192A ILE* 4.0 32.1 - - + -
228A LEU* 4.3 22.4 - - + -
232A ILE* 4.6 4.3 - - + -
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Residues in contact with PHE 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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101A ASN* 3.5 25.4 - - + +
103A ILE* 4.2 9.2 - - + -
151A MET* 3.1 46.0 - - + -
152A VAL* 1.3 73.4 - - - +
154A ASP* 1.3 62.4 + - - +
155A MET* 3.6 16.6 + - - +
171A TYR* 5.2 2.9 - + - -
175A PHE* 4.8 12.6 - + - -
189A LEU* 3.7 37.7 - - + -
190A ILE 2.7 17.7 + - - +
191A VAL* 3.6 8.0 - - + -
192A ILE* 3.0 29.8 + - - +
518A 11A 3.9 30.5 - - + -
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Residues in contact with ASP 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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100A PHE* 6.2 0.4 - - + -
101A ASN 2.9 13.2 + - - +
102A ILE* 3.9 28.2 - - + +
103A ILE* 3.2 7.6 + - - -
104A GLY 3.1 20.8 + - - -
105A SER* 5.4 0.9 + - - -
152A VAL* 3.9 2.3 + - + -
153A PHE* 1.3 70.4 - - - +
155A MET* 1.3 62.4 + - - +
156A GLU* 3.2 13.9 + - - +
192A ILE* 3.7 14.6 - - + +
193A ARG* 2.8 48.5 + - - +
241A PHE* 3.9 9.2 - - + -
260A TYR* 5.5 1.7 - - - -
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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