Contacts of the strand formed by residues 150 - 156 (chain K) in PDB entry 5T0G
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 GLY 150 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146K VAL* 3.6 11.0 - - - -
147K ASP* 2.7 40.4 + - - +
148K GLU 3.4 1.6 - - - -
149K LYS* 1.3 80.3 - - - +
151K PRO* 1.3 75.7 - - - +
152K GLN* 3.3 0.6 + - - -
222K PRO* 5.2 1.8 - - - -
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Residues in contact with PRO 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K GLN* 2.8 26.0 + - - +
42K THR 3.0 27.5 - - - +
43K SER* 3.2 22.2 - - - +
44K GLU 4.1 1.1 - - - -
45K GLY* 3.6 15.0 - - - +
46K VAL* 3.6 17.3 - - + -
145K GLY 3.7 6.1 - - - +
146K VAL* 3.8 11.0 - - + -
149K LYS 4.8 0.2 - - - +
150K GLY* 1.3 82.3 - - - +
152K GLN* 1.3 58.8 + - - +
222K PRO* 4.4 14.4 - - + -
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Residues in contact with GLN 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K GLN* 2.5 25.3 + - - +
46K VAL* 3.4 9.0 - - - +
109K VAL* 4.3 9.7 - - + +
143K PHE 3.9 1.0 - - - +
144K GLY* 3.6 1.4 - - - -
145K GLY 2.8 38.1 + - - +
147K ASP* 3.1 31.4 + - - +
149K LYS* 3.9 31.9 + - - +
151K PRO* 1.3 81.3 + - - +
153K LEU* 1.3 59.3 + - - +
154K PHE* 4.2 20.8 - - + -
164K GLN* 3.4 22.2 + - - +
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Residues in contact with LEU 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K GLY* 3.4 32.5 - - - +
40K ILE 3.4 7.6 - - - +
41K GLN* 3.1 27.0 + - + +
46K VAL* 4.2 10.3 - - + -
48K LEU* 4.4 15.7 - - + -
142K LEU* 4.7 4.5 - - + -
143K PHE 3.2 24.0 - - - +
144K GLY* 4.0 7.0 - - - -
152K GLN* 1.3 73.8 - - - +
154K PHE* 1.3 77.0 + - - +
164K GLN* 4.1 0.9 - - - +
165K CYS 2.8 28.3 + - - +
166K ASP 3.4 18.6 - - - +
168K ARG* 4.5 8.1 - - + +
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Residues in contact with PHE 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K VAL* 3.6 27.6 - - + -
110K GLU* 3.5 39.5 - - + -
113K THR* 3.9 11.0 - - - +
142K LEU* 3.4 5.7 - - - +
143K PHE* 2.6 50.5 + - + +
147K ASP* 5.3 3.1 - - - -
149K LYS* 5.8 4.9 - - - -
152K GLN* 4.2 20.0 - - + -
153K LEU* 1.3 91.0 - - - +
155K HIS* 1.3 59.8 + - - +
162K PHE* 3.5 27.4 - + + -
163K VAL 4.5 1.6 - - - -
164K GLN* 3.6 36.3 - - + -
165K CYS* 4.9 1.3 - - - -
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Residues in contact with HIS 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140K ALA* 4.3 7.0 - - + -
141K LEU 3.5 2.9 + - - -
142K LEU* 3.4 16.6 - - + +
143K PHE* 6.0 0.7 - - - -
154K PHE* 1.3 75.9 - - - +
156K MET* 1.3 91.8 + - - +
157K ASP* 4.5 7.7 + - + +
161K THR 6.0 0.2 - - - -
162K PHE* 3.4 5.5 - - - -
163K VAL* 2.9 54.8 + - + +
165K CYS* 4.0 9.3 - - + +
168K ARG* 3.7 44.1 + - + -
170K ILE* 4.0 22.4 - - + -
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Residues in contact with MET 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K THR* 5.1 4.7 - - + +
116K VAL* 3.5 45.5 - - + +
117K SER* 4.8 5.2 - - - +
120K ALA* 4.8 5.2 - - + -
139K VAL 6.0 0.4 - - - +
140K ALA* 3.7 0.7 - - - +
141K LEU* 2.9 55.8 + - + +
143K PHE* 4.2 14.8 - - + -
155K HIS* 1.3 90.4 + - - +
157K ASP* 1.3 81.5 + - - +
158K PRO* 5.4 1.6 - - + -
160K GLY* 4.2 15.0 - - - -
161K THR 4.0 9.9 - - - +
162K PHE* 4.7 11.4 - - + -
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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