Contacts of the strand formed by residues 137 - 142 (chain B) in PDB entry 5T1I
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 MET 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA* 3.3 6.4 - - - +
130B THR* 2.9 49.1 + - + +
133B SER* 4.2 15.7 - - - +
135B GLU 3.8 7.9 - - - +
136B LEU* 1.3 81.3 - - - +
138B PHE* 1.3 65.3 + - - +
150B LEU* 4.4 31.9 - - + +
151B VAL* 3.2 13.7 - - - +
152B LEU* 3.9 34.8 - - + +
153B ALA 4.1 0.4 - - - +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.7 39.9 - - + -
128B GLY 3.5 4.9 - - - -
129B ALA* 4.3 4.5 - - + -
136B LEU* 4.2 10.8 - - + -
137B MET* 1.3 77.4 - - - +
139B LEU* 1.3 60.0 - - - +
140B MET 3.5 0.7 + - - -
149B ASP 3.4 1.6 - - - +
150B LEU* 3.4 5.6 - - - -
151B VAL* 2.9 40.4 + - + +
152B LEU 4.8 0.4 - - - -
153B ALA* 3.5 36.3 - - + -
156B ALA* 3.8 10.5 - - + -
157B ASN* 4.4 0.9 - - - -
164B VAL* 3.9 25.4 - - + -
167B PHE* 4.0 21.8 - + - -
168B TYR* 3.3 33.0 - + - -
48C LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.5 2.8 - - - -
127B ILE* 2.9 53.2 + - + +
128B GLY* 2.9 25.6 + - - +
129B ALA 4.4 0.2 - - - +
138B PHE* 1.3 68.7 - - - +
140B MET* 1.3 57.8 + - - +
148B ALA* 3.8 19.3 - - + +
149B ASP* 3.6 23.6 - - - +
150B LEU* 4.1 14.1 - - + +
51C ILE* 4.0 22.4 - - + -
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PHE* 4.3 10.3 - - + -
123B PRO* 3.7 15.7 - - + -
125B ARG 3.7 22.2 - - - +
126B ILE* 3.7 22.4 - - + +
138B PHE 3.5 0.8 + - - -
139B LEU* 1.3 71.2 - - - +
141B LYS* 1.3 67.4 + - - +
142B TRP* 3.7 38.9 + - + -
148B ALA* 3.1 8.1 - - - -
149B ASP 2.8 35.1 + - - +
151B VAL* 4.3 15.7 - - + -
156B ALA* 4.7 1.8 - - + -
160B CYS* 3.8 29.4 - - - -
163B ILE* 4.1 3.1 - - + -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 2.8 54.0 + - - +
125B ARG* 2.8 32.7 + - + +
127B ILE* 4.0 22.6 - - + +
139B LEU 3.9 1.4 + - - -
140B MET* 1.3 75.1 - - - +
142B TRP* 1.3 69.0 + - - +
144B ASP* 4.2 3.0 - - - +
145B SER 2.5 37.0 + - - +
146B ASP* 4.5 13.2 - - - +
148B ALA* 4.4 10.0 - - + +
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Residues in contact with TRP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY* 3.5 32.1 - - - -
117B PHE* 3.5 42.0 - + - -
119B ARG* 3.5 16.1 - - - +
121B LEU* 3.6 46.4 - - + -
122B ASP 3.5 3.8 - - - -
123B PRO* 3.6 26.7 - - + -
124B GLU* 4.0 1.6 - - - -
140B MET* 3.7 28.0 + - + -
141B LYS* 1.3 100.8 + - - +
143B LYS* 1.4 61.8 + - - +
145B SER* 3.2 8.5 + - - +
147B GLU 3.6 10.5 + - - -
149B ASP* 2.7 31.2 + - + +
151B VAL* 3.9 8.1 - - + -
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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