Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 6ACQ
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 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B HIS 4.1 0.5 - - - +
139B PHE* 5.2 0.5 - - - -
140B PHE* 3.3 51.1 + - + +
146B MET* 3.5 5.9 - - + +
147B LYS* 1.3 80.3 - - - +
149B VAL* 1.3 68.6 + - - +
150B GLU* 4.5 1.6 - - + -
175B ASP 3.5 16.2 - - - +
177B VAL* 3.9 32.5 - - + -
187B VAL* 3.9 4.5 - - + -
214C LYS* 4.7 0.2 - - + -
215C ALA* 3.5 35.4 - - + +
218C LEU* 3.8 28.3 + - + +
219C GLY* 3.5 11.7 - - - +
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Residues in contact with VAL 149 (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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137B MET* 4.4 13.5 - - + -
138B HIS 3.4 15.7 - - - +
139B PHE* 3.8 31.0 - - + -
148B LEU* 1.3 82.7 - - - +
150B GLU* 1.3 63.9 + - - +
151B VAL* 3.4 19.8 + - + -
169B SER* 4.2 13.9 - - - +
172B ILE* 5.9 0.2 - - + -
174B LYS* 3.9 22.0 - - + -
175B ASP 3.2 6.9 + - - +
176B PRO* 3.2 8.8 - - + +
177B VAL* 2.9 27.7 + - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B HIS* 2.9 58.6 + - + +
140B PHE* 3.6 11.8 - - + -
148B LEU* 4.2 5.1 - - + -
149B VAL* 1.3 71.0 - - - +
151B VAL* 1.3 58.8 + - - +
152B ILE* 3.1 19.4 + - + +
177B VAL* 3.6 22.0 - - + -
179B VAL* 4.4 3.8 - - + -
184B GLY 4.7 0.3 - - - +
185B PHE* 3.5 18.8 - - - +
186B VAL* 3.0 17.3 + - - +
187B VAL* 3.0 40.0 + - + +
188B ASN 5.3 0.3 + - - -
215C ALA* 5.0 0.2 - - + -
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Residues in contact with VAL 151 (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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135B ILE* 3.6 23.1 - - + -
136B GLY 3.5 7.0 - - - +
137B MET* 4.8 0.7 - - - +
149B VAL* 3.4 10.1 + - + -
150B GLU* 1.3 69.8 - - - +
152B ILE* 1.3 57.0 - - - +
153B ARG* 3.5 2.1 + - + +
162B PHE* 3.4 35.0 - - + -
165B VAL* 4.0 22.0 - - + +
166B LYS* 5.1 1.3 - - - -
169B SER* 4.6 0.4 - - - +
176B PRO* 3.8 25.4 - - + -
177B VAL 2.9 17.4 + - - +
178B GLU* 3.8 0.3 - - - -
179B VAL 2.9 28.1 + - - +
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Residues in contact with ILE 152 (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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116B THR 5.5 0.9 - - - +
121B ILE* 3.6 18.6 - - + +
135B ILE* 3.2 5.7 - - - +
136B GLY* 2.8 49.0 + - - -
138B HIS* 4.5 2.2 - - + -
150B GLU* 3.1 27.8 - - + +
151B VAL* 1.3 71.0 - - - +
153B ARG* 1.3 62.7 + - - +
154B GLY 3.7 1.0 + - - -
179B VAL* 3.4 15.0 - - + +
180B ALA 4.8 0.2 - - - -
181B GLU* 3.8 22.2 - - + +
185B PHE* 3.4 60.8 - - + -
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Residues in contact with ARG 153 (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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135B ILE* 4.3 3.6 - - + -
151B VAL 4.7 1.3 - - - +
152B ILE* 1.3 72.1 - - - +
154B GLY* 1.3 65.5 + - - +
157B THR* 3.3 34.3 + - + +
158B SER* 4.4 0.2 - - - +
159B GLN* 2.9 47.0 + - - +
162B PHE* 3.5 39.2 - - + +
178B GLU* 3.1 31.1 + - + -
179B VAL 2.6 17.9 + - - +
180B ALA* 3.8 5.2 - - + -
181B GLU* 2.9 26.3 + - - +
262F LYS* 5.1 0.5 + - - -
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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