Contacts of the strand formed by residues 138 - 148 (chain B) in PDB entry 5T78
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 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASN* 2.8 23.8 + - - +
137B SER* 1.3 88.4 - - - +
139B VAL* 1.3 59.5 - - - +
185B THR* 3.5 26.0 - - + -
186B VAL* 3.5 5.2 - - - +
187B PRO* 3.8 26.7 - - + -
188B SER* 3.0 5.0 + - - -
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Residues in contact with VAL 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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129B PRO* 4.1 15.0 - - + -
138B MET* 1.3 75.6 - - - +
140B THR* 1.3 67.0 - - - +
141B LEU* 3.9 21.8 - - + -
184B VAL 4.0 0.2 - - - +
185B THR* 3.2 4.4 - - - +
186B VAL* 2.8 63.0 + - + +
187B PRO 4.0 7.6 - - - +
188B SER* 4.2 11.7 - - - +
191B TRP* 4.5 19.7 - - + +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR* 5.1 8.7 - - - +
121A SER* 3.7 25.7 + - - +
123A PHE* 3.3 19.5 - - + -
140A PHE* 4.1 10.1 - - + -
142A ASN* 3.9 12.9 + - - +
129B PRO* 4.3 3.1 - - - +
139B VAL* 1.3 76.1 - - - +
141B LEU* 1.3 72.6 + - - +
183B SER* 3.7 22.7 - - - +
184B VAL 3.4 3.6 - - - +
185B THR* 3.0 20.8 + - - +
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Residues in contact with LEU 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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123A PHE* 4.2 6.1 - - - -
140A PHE* 4.0 0.5 - - - -
127B LEU 3.9 9.2 - - - +
129B PRO* 3.6 26.0 - - + -
139B VAL* 3.9 17.9 - - + +
140B THR* 1.3 85.0 - - - +
142B GLY* 1.3 61.0 + - - +
183B SER* 3.5 4.7 - - - -
184B VAL* 2.7 43.3 + - + +
186B VAL* 4.9 5.8 - - + -
191B TRP* 3.7 50.7 - - + +
196B VAL* 4.1 19.1 - - + -
213B ILE* 4.1 11.2 - - + -
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Residues in contact with GLY 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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140A PHE* 4.0 3.1 - - - -
127B LEU* 2.8 47.3 + - - +
141B LEU* 1.3 80.2 - - - +
143B CYS* 1.3 58.9 + - - -
157B TRP* 3.6 7.2 - - - -
182B SER 3.1 11.9 - - - -
213B ILE* 3.7 13.3 - - - +
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Residues in contact with CYS 143 (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 VAL* 3.5 23.6 - - - -
125B TYR 3.6 7.6 - - - -
127B LEU* 3.8 4.9 - - - +
142B GLY* 1.3 75.0 - - - -
144B LEU* 1.3 59.5 + - - +
145B VAL* 4.0 6.1 + - + +
155B VAL* 4.9 0.2 - - + -
157B TRP* 3.9 7.9 - - + -
181B SER* 3.3 8.7 - - - -
182B SER* 3.0 31.7 + - - +
198B CYS* 2.0 52.5 - - + -
200B VAL* 4.6 0.4 - - - -
211B LYS* 4.8 3.1 - - - -
213B ILE* 4.9 1.8 - - - -
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Residues in contact with LEU 144 (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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129A GLN* 4.5 4.0 - - - +
136A SER* 3.6 34.1 - - - +
138A VAL* 4.3 17.3 - - + -
183A THR* 4.5 7.6 - - + +
123B SER 3.5 2.3 - - - +
124B VAL* 3.3 4.6 - - - -
125B TYR* 2.8 62.5 + - + +
127B LEU* 4.0 15.0 - - + +
143B CYS* 1.3 70.7 - - - +
145B VAL* 1.3 61.3 + - - +
146B LYS* 3.8 11.1 + - + -
179B THR* 4.1 17.3 - - + -
180B LEU 3.8 13.2 - - - +
181B SER* 3.9 13.0 - - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 3.5 28.0 - - + -
123B SER 3.5 2.9 - - - -
124B VAL* 4.4 5.8 - - + +
143B CYS* 4.7 6.5 - - + +
144B LEU* 1.3 76.7 - - - +
146B LYS* 1.3 58.5 + - - +
148B TYR* 3.8 14.9 - - + -
153B VAL* 4.4 5.8 - - + -
155B VAL* 4.1 6.1 - - + -
179B THR* 3.3 4.4 - - - +
180B LEU* 2.9 57.5 + - + +
182B SER 5.8 0.4 - - - +
200B VAL* 3.9 36.8 - - + -
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Residues in contact with LYS 146 (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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129A GLN* 3.9 26.0 - - - +
136A SER* 4.0 11.8 + - - +
183A THR* 5.9 1.2 - - - +
185A THR* 4.2 19.0 + - - +
122B PRO* 3.7 0.5 - - - +
123B SER* 2.9 41.2 + - - +
125B TYR* 4.1 18.2 - - + +
144B LEU* 4.5 9.6 - - + -
145B VAL* 1.3 74.1 - - - +
147B GLY* 1.3 67.1 + - - +
148B TYR* 3.7 2.5 - - - -
179B THR* 3.8 22.6 + - + +
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Residues in contact with GLY 147 (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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120B THR* 3.3 23.7 - - - +
121B PRO 3.6 5.5 - - - +
146B LYS* 1.3 80.7 - - - +
148B TYR* 1.3 57.4 + - - -
177B LEU* 3.9 26.1 - - - +
178B TYR 2.9 15.8 + - - -
179B THR* 3.6 1.9 + - - -
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Residues in contact with TYR 148 (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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120B THR 3.2 13.2 - - - +
122B PRO* 3.6 20.4 - - + -
145B VAL* 3.8 36.1 - - + -
147B GLY* 1.3 79.7 - - - +
149B PHE* 1.3 63.6 + - - +
150B PRO 3.6 15.0 - - - -
151B GLU* 3.4 19.2 + - + -
153B VAL* 3.4 26.4 - - + +
171B ALA* 3.1 26.7 - - - +
177B LEU* 3.7 2.7 - - - -
178B TYR* 2.8 58.7 + - + +
179B THR* 4.2 1.8 - - - -
180B LEU* 3.3 15.7 - - + +
202B HIS* 4.0 2.5 - - - +
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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