Contacts of the strand formed by residues 148 - 160 (chain A) in PDB entry 4MEI
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 ILE 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PHE 3.5 10.3 - - - +
105A GLN* 3.9 37.9 - - + +
147A MET* 1.3 82.8 - - - +
149A ALA* 1.3 63.4 + - - +
150A THR* 4.0 16.6 - - - +
171A THR 3.5 2.6 - - - +
172A VAL* 3.3 1.8 - - - -
173A ARG* 2.7 73.7 + - + +
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Residues in contact with ALA 149 (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 GLY* 3.6 5.6 - - - -
104A PHE 2.9 39.0 + - - +
144A TYR* 3.9 40.5 - - + -
148A ILE* 1.3 73.8 - - - +
150A THR* 1.3 64.2 + - - +
151A VAL 4.2 0.2 - - - -
170A LYS* 4.2 8.1 - - + -
171A THR 3.5 4.3 - - - -
172A VAL* 4.1 8.7 - - + +
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Residues in contact with THR 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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99A ARG* 3.7 22.2 - - - +
148A ILE* 4.0 13.9 - - - +
149A ALA* 1.3 76.0 + - - +
151A VAL* 1.3 68.3 + - - +
152A THR* 3.7 5.3 + - - +
169A TYR 3.8 0.2 - - - +
170A LYS* 3.4 3.0 - - - -
171A THR* 2.8 47.7 + - - +
173A ARG* 5.3 3.8 + - - -
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Residues in contact with VAL 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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98A VAL* 4.7 1.6 - - + -
99A ARG* 3.1 65.0 + - + +
102A GLU* 3.8 19.5 - - + +
103A GLY* 3.7 27.1 - - - +
149A ALA 4.3 0.2 + - - -
150A THR* 1.3 76.2 - - - +
152A THR* 1.3 66.6 + - - +
153A ILE* 4.2 5.4 - - + -
168A TYR* 3.7 33.7 - - + -
169A TYR 3.4 4.5 - - - -
170A LYS* 4.5 3.6 - - + +
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Residues in contact with THR 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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99A ARG* 5.1 0.4 - - - +
150A THR* 3.7 5.1 + - - +
151A VAL* 1.3 75.3 + - - +
153A ILE* 1.3 73.2 + - - +
154A LYS 3.4 0.2 + - - -
168A TYR* 3.2 3.1 - - - +
169A TYR* 2.8 79.3 + - + +
171A THR* 4.7 3.3 + - - -
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Residues in contact with ILE 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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95A SER* 4.2 31.9 - - - +
98A VAL* 4.8 2.2 - - + -
99A ARG* 4.3 15.1 - - + +
151A VAL* 4.1 15.9 + - + -
152A THR* 1.3 83.1 - - - +
154A LYS* 1.3 64.6 + - - +
155A SER* 3.6 15.7 - - - +
156A ILE* 4.0 21.3 - - + -
166A VAL* 3.5 26.2 - - + -
167A ARG 4.1 0.4 - - - +
168A TYR* 4.1 3.1 - - + -
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Residues in contact with LYS 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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152A THR 3.4 1.4 + - - -
153A ILE* 1.3 74.1 - - - +
155A SER* 1.3 62.6 + - - +
167A ARG* 2.8 38.0 + - + +
168A TYR 3.9 17.7 + - - +
169A TYR* 3.7 31.6 - - + -
183A HIS* 3.2 32.6 + - + +
219A GLU* 3.3 25.3 + - - -
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Residues in contact with SER 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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153A ILE* 3.6 3.6 - - - +
154A LYS* 1.3 80.8 - - - +
156A ILE* 1.3 68.4 + - - +
157A SER* 5.3 3.1 + - - -
165A GLN 3.7 1.0 - - - +
166A VAL* 3.4 5.0 - - - +
167A ARG* 2.9 64.4 + - - +
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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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91A ARG* 2.7 86.4 + - + +
94A ALA* 4.7 2.0 - - + -
95A SER* 3.8 25.4 - - - +
153A ILE* 4.0 14.8 - - + -
155A SER* 1.3 81.4 - - - +
157A SER* 1.3 59.1 + - - +
158A PHE* 5.3 1.8 - - + -
164A ILE* 3.7 26.0 - - + -
165A GLN 3.4 4.3 - - - +
166A VAL* 4.4 8.5 - - + -
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Residues in contact with SER 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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91A ARG* 4.4 6.1 - - - +
155A SER* 4.3 3.8 + - - -
156A ILE* 1.3 75.2 - - - +
158A PHE* 1.3 67.2 + - - +
159A ILE* 5.8 0.2 - - - +
164A ILE* 3.4 4.0 - - - +
165A GLN* 2.7 58.3 + - - +
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Residues in contact with PHE 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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87A GLU* 3.8 26.9 - - + -
90A THR* 4.2 16.6 - - + -
91A ARG* 3.6 37.9 - - + -
156A ILE* 5.3 2.2 - - + -
157A SER* 1.3 81.2 - - - +
159A ILE* 1.3 63.9 + - - +
160A SER 3.6 20.9 - - - +
161A LYS* 4.7 3.6 - - - -
163A LEU 3.5 2.9 - - - -
164A ILE* 3.8 31.0 - - + -
190A PHE* 4.1 15.7 - + - -
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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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157A SER* 3.9 0.6 + - - +
158A PHE* 1.3 74.4 - - - +
160A SER* 1.3 59.8 + - - +
163A LEU* 2.7 30.6 + - + +
165A GLN* 3.9 29.6 - - + +
187A ILE* 4.1 32.1 - - + -
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Residues in contact with SER 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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158A PHE* 3.6 17.4 - - - +
159A ILE* 1.3 81.7 - - - +
161A LYS* 1.3 64.3 + - - +
162A ASP* 3.1 22.2 + - - -
163A LEU* 3.2 28.8 + - - +
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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