Contacts of the strand formed by residues 149 - 158 (chain A) in PDB entry 5TIN
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 VAL 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ASP* 5.0 1.6 - - - +
147A MET 5.6 0.4 - - - +
148A ASP* 1.3 75.5 - - - +
150A GLN* 1.3 74.1 + - - +
151A THR* 5.5 0.6 + - - +
190A LYS* 6.0 1.3 - - + -
215A HIS* 4.8 11.9 - - + +
216A LEU 3.3 25.6 - - - +
217A GLU* 4.3 10.1 - - + -
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Residues in contact with GLN 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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138A CYS* 4.9 2.5 - - - -
139A PRO 4.4 1.7 - - - +
140A MET* 3.3 30.7 - - + -
141A ASP* 2.8 46.3 + - - +
142A LEU* 4.0 5.7 - - - +
148A ASP* 2.8 32.6 + - - +
149A VAL* 1.3 80.6 + - - +
151A THR* 1.3 63.1 + - - +
152A CYS* 4.1 13.2 - - - -
187A PHE* 4.9 7.9 - - + -
214A PHE 3.7 0.2 - - - +
215A HIS* 3.6 3.5 - - - -
216A LEU* 2.9 43.3 + - + +
218A ARG* 4.8 3.4 - - - +
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Residues in contact with THR 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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138A CYS* 3.5 9.0 - - - -
139A PRO* 4.7 6.4 - - - +
149A VAL* 5.5 0.9 + - - +
150A GLN* 1.3 75.0 + - - +
152A CYS* 1.3 63.5 + - - +
153A ILE* 4.1 7.2 + - + +
213A ARG* 3.8 43.7 - - + +
214A PHE 3.3 10.1 - - - +
215A HIS* 3.3 26.4 + - + -
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Residues in contact with CYS 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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48A PHE* 5.2 0.2 - - + -
51A ILE* 5.6 0.7 - - - -
58A TYR* 3.6 28.7 - - + -
138A CYS* 2.1 46.7 - - - -
140A MET* 5.0 4.7 - - - -
150A GLN* 4.1 5.1 - - - -
151A THR* 1.3 73.7 - - - +
153A ILE* 1.3 61.7 + - - +
213A ARG* 3.6 0.2 - - - -
214A PHE* 2.8 40.9 + - + +
216A LEU* 3.7 28.9 - - + +
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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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58A TYR* 2.7 25.3 + - - -
102A ASN* 2.9 33.3 + - + +
136A LEU* 4.4 0.2 - - - +
137A SER 4.9 4.1 + - - +
138A CYS* 5.0 1.2 - - - +
139A PRO* 6.4 2.0 - - + -
151A THR* 4.5 6.7 - - + +
152A CYS* 1.3 77.2 - - - +
154A MET* 1.3 58.2 + - - +
155A GLN* 3.8 34.3 - - + +
211A GLU* 4.1 11.2 - - + +
212A VAL 3.3 8.1 - - - +
213A ARG* 3.9 37.0 - - + +
214A PHE* 5.1 0.2 - - - -
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Residues in contact with MET 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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43A ILE* 3.9 27.8 - - + -
45A ILE* 5.4 0.9 - - + -
58A TYR* 4.0 3.4 - - - +
60A VAL* 4.0 20.6 - - + -
62A ILE* 4.5 10.3 - - + -
100A PHE* 3.9 28.7 - - + -
102A ASN* 3.8 3.6 - - - -
134A LEU* 4.7 0.7 - - + -
136A LEU* 3.8 24.0 - - + -
153A ILE* 1.3 75.1 - - - +
155A GLN* 1.3 63.0 + - - +
156A LEU* 3.8 17.4 - - + +
211A GLU* 3.3 3.9 - - - -
212A VAL* 3.0 39.0 + - + -
214A PHE* 4.1 19.5 - - + -
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Residues in contact with GLN 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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100A PHE* 3.2 10.4 - - - +
101A ALA* 3.1 36.8 + - + +
102A ASN* 3.1 18.3 + - - +
153A ILE* 3.8 23.9 - - + +
154A MET* 1.3 75.5 - - - +
156A LEU* 1.3 61.4 + - - +
157A GLU 4.0 0.2 - - - -
198A CYS* 3.5 18.6 - - - +
200A LYS* 3.2 26.5 + - - +
209A CYS* 4.0 6.7 - - - -
210A ILE 3.5 3.4 - - - -
211A GLU* 3.0 26.3 + - + +
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Residues in contact with LEU 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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41A CYS* 4.3 12.1 - - + -
43A ILE* 4.8 1.6 - - + -
64A LEU* 4.0 18.6 - - + -
98A LEU* 4.0 27.1 - - + -
99A PHE 3.7 4.0 - - - -
100A PHE* 3.8 24.2 - - + -
154A MET* 3.8 21.8 - - + +
155A GLN* 1.3 76.5 - - - +
157A GLU* 1.3 59.4 + - - +
168A PHE* 3.6 9.1 - - + -
170A TRP* 4.0 28.7 - - + -
209A CYS* 3.2 2.2 - - - -
210A ILE* 2.7 45.5 + - + +
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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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98A LEU* 3.3 4.5 - - - -
99A PHE* 2.8 62.0 + - + +
101A ALA* 3.3 11.1 - - + +
156A LEU* 1.3 73.9 - - - +
158A SER* 1.3 73.5 + - - +
168A PHE* 3.5 6.9 - - - -
200A LYS* 2.8 39.4 + - + +
202A TYR* 2.7 33.8 + - - -
207A PHE* 4.6 2.4 - - + +
208A THR 3.4 14.6 - - - +
209A CYS* 3.8 7.1 - - + -
63B PHE* 4.8 0.2 - - - -
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Residues in contact with SER 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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97A ASP* 2.8 23.5 + - - -
99A PHE* 3.7 1.5 - - - -
157A GLU* 1.3 85.2 - - - +
159A PHE* 1.3 58.6 + - - +
161A TYR* 3.1 35.8 + - - +
166A LEU* 3.9 10.3 - - - -
168A PHE* 3.6 4.5 - - - -
207A PHE* 3.4 15.0 - - - +
208A THR* 3.2 28.9 + - - -
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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