Contacts of the strand formed by residues 163 - 173 (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 LEU 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PHE* 3.5 1.0 - - - -
159A ILE* 2.7 51.7 + - + +
160A SER* 3.2 30.6 + - - +
161A LYS 3.7 0.2 - - - -
162A ASP* 1.3 79.9 - - - +
164A ILE* 1.3 57.5 + - - +
187A ILE* 3.4 33.2 - - + -
188A LEU 3.4 12.6 - - - +
189A ASN* 4.2 15.5 - - + +
190A PHE* 3.8 1.4 - - - -
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Residues in contact with ILE 164 (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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90A THR* 3.8 23.1 - - + +
94A ALA* 4.1 18.4 - - + -
156A ILE* 3.7 24.5 - - + -
157A SER 3.4 11.0 - - - +
158A PHE* 3.8 14.4 - - + +
159A ILE* 5.2 0.9 - - - -
163A LEU* 1.3 73.6 - - - +
165A GLN* 1.3 63.9 + - - +
166A VAL* 4.1 13.0 - - + -
186A SER 3.7 0.7 - - - +
187A ILE* 3.4 6.9 - - - +
188A LEU* 2.9 41.1 + - + +
190A PHE* 3.4 39.7 - - + -
209A PHE* 5.1 2.2 - - + -
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Residues in contact with GLN 165 (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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155A SER 3.7 1.7 - - - +
156A ILE* 3.4 4.2 - - - -
157A SER* 2.7 49.7 + - - +
159A ILE* 3.9 26.4 - - + +
164A ILE* 1.3 75.4 - - - +
166A VAL* 1.3 63.5 + - - +
167A ARG* 3.6 23.7 + - + +
185A VAL* 3.6 30.2 - - + +
186A SER 3.4 2.9 - - - -
187A ILE* 4.0 9.9 - - + -
219A GLU* 5.5 0.2 + - - -
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Residues in contact with VAL 166 (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 ALA* 4.4 12.6 - - + +
98A VAL* 3.9 35.0 - - + -
153A ILE* 3.5 31.6 - - + -
155A SER 3.4 7.2 - - - +
156A ILE* 4.4 10.1 - - + -
164A ILE* 4.1 13.0 - - + -
165A GLN* 1.3 75.8 - - - +
167A ARG* 1.3 63.3 + - - +
168A TYR* 3.6 7.1 - - + -
185A VAL* 3.4 1.6 - - - -
186A SER* 2.8 37.6 + - - +
188A LEU* 4.1 13.0 - - + -
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Residues in contact with ARG 167 (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* 3.9 1.9 - - - +
154A LYS* 2.8 48.3 + - + +
155A SER* 2.9 39.5 + - - +
165A GLN* 3.6 31.2 - - + +
166A VAL* 1.3 72.5 - - - +
168A TYR* 1.3 62.6 + - - +
184A TRP 3.3 7.4 - - - +
185A VAL* 4.0 9.4 - - + -
219A GLU* 2.9 38.6 + - - +
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Residues in contact with TYR 168 (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* 3.6 14.6 - - + -
102A GLU* 3.3 26.9 + - + +
151A VAL* 3.7 26.2 - - + -
152A THR 3.2 16.6 - - - +
153A ILE* 4.1 6.7 - - + -
154A LYS* 3.9 10.6 + - - +
166A VAL* 3.6 14.1 - - + -
167A ARG* 1.3 74.9 - - - +
169A TYR* 1.3 69.3 + - - +
170A LYS* 3.9 13.5 + - - -
183A HIS* 3.6 0.9 - - - -
184A TRP* 2.9 69.9 + + + +
186A SER* 3.3 21.1 - - - -
216A SER* 2.6 22.2 + - - -
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Residues in contact with TYR 169 (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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151A VAL* 3.4 2.8 - - - -
152A THR* 2.8 72.7 + - + +
154A LYS* 3.7 22.0 - - + -
168A TYR* 1.3 80.6 - - - +
170A LYS* 1.3 56.9 + - - +
171A THR* 3.4 24.5 - - - -
181A ILE* 4.0 21.5 - - + -
182A SER 3.1 16.6 - - - +
183A HIS* 3.6 26.0 - + + +
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Residues in contact with LYS 170 (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 GLU* 3.4 44.5 + - - +
144A TYR* 3.1 32.7 + - + +
149A ALA* 4.2 12.3 - - + -
150A THR 3.4 12.1 - - - +
151A VAL* 4.5 3.1 - - + +
168A TYR* 3.9 14.7 + - + -
169A TYR* 1.3 72.3 - - - +
171A THR* 1.3 64.5 + - - +
172A VAL* 4.0 7.7 - - + +
180A THR 3.8 0.7 - - - +
181A ILE* 3.4 7.1 - - - +
182A SER* 2.8 37.1 + - - +
184A TRP* 3.6 33.3 - - - +
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Residues in contact with THR 171 (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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148A ILE 3.5 2.9 - - - +
149A ALA* 3.5 1.7 - - - -
150A THR* 2.8 40.8 + - - -
152A THR* 4.7 2.5 + - - -
169A TYR* 3.4 26.7 - - - -
170A LYS* 1.3 71.4 + - - +
172A VAL* 1.3 60.4 + - - +
173A ARG* 5.2 2.3 - - + +
179A GLU* 3.7 41.7 - - + +
180A THR 3.5 4.9 - - - +
181A ILE* 4.2 10.1 - - + +
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Residues in contact with VAL 172 (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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144A TYR* 3.6 35.4 - - + +
147A MET* 3.7 36.5 - - + +
148A ILE 3.3 7.0 - - - +
149A ALA* 4.1 7.6 - - + -
170A LYS* 4.4 11.7 - - + +
171A THR* 1.3 74.4 - - - +
173A ARG* 1.3 62.3 + - - +
178A LYS 3.7 2.4 - - - +
179A GLU* 3.4 5.2 - - - -
180A THR* 2.9 45.9 + - + +
182A SER* 5.8 1.8 - - - +
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Residues in contact with ARG 173 (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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147A MET* 3.2 10.3 - - - +
148A ILE* 2.7 72.2 + - - +
150A THR* 5.3 4.0 + - - -
171A THR* 5.2 2.7 - - + +
172A VAL* 1.3 76.9 - - - +
174A ASP* 1.3 64.9 + - - +
177A GLU* 3.7 43.9 + - - +
178A LYS 4.4 1.8 - - - -
179A GLU* 4.1 23.6 + - + +
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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