Contacts of the strand formed by residues 139 - 146 (chain B) in PDB entry 6CU0
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ALA* 1.3 79.6 - - - +
140B VAL* 1.3 60.7 + - - -
141B TYR* 3.7 7.8 - - - -
205B HIS* 3.4 8.7 + - - -
206B LEU* 2.8 34.7 + - - +
241B THR* 4.4 13.7 - - - -
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Residues in contact with VAL 140 (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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92A PHE* 3.6 36.6 - - + -
119A SER* 5.5 5.8 - - - +
139B GLY* 1.3 74.5 - - - -
141B TYR* 1.3 67.1 + - - +
203B LEU* 4.0 28.9 - - + -
204B LEU 3.5 9.4 - - - +
205B HIS* 4.0 22.9 - - + +
239B ARG* 3.8 1.2 - - - +
240B VAL* 2.9 25.7 + - + -
241B THR* 3.2 20.8 + - - +
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Residues in contact with TYR 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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91B MET* 3.2 28.7 - - + +
124B LEU* 5.0 0.7 - - + -
135B VAL* 3.5 11.3 - - + +
137B LYS* 2.6 30.0 + - - +
138B ALA 4.2 2.1 + - - -
139B GLY* 3.7 23.8 - - - -
140B VAL* 1.3 78.8 - - - +
142B TYR* 1.3 61.5 + - - +
143B VAL* 3.5 17.9 + - + +
203B LEU* 3.2 7.8 - - - -
204B LEU 2.8 33.8 + - - +
206B LEU* 3.5 23.6 - - + -
237B LEU* 4.1 20.9 - - + -
238B PHE 3.3 8.7 - - - +
239B ARG* 3.4 36.5 - - + +
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Residues in contact with TYR 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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142A TYR* 3.3 24.7 + + - -
144A PHE* 4.1 12.6 - + - -
199A PHE* 3.2 25.5 - - - -
238A PHE* 3.9 15.5 - + + -
141B TYR* 1.3 69.4 - - - +
143B VAL* 1.3 58.5 + - - +
144B PHE* 3.9 16.6 - + + -
199B PHE* 3.8 5.0 - - - -
201B GLY* 3.9 21.0 - - - -
202B ARG* 3.6 15.5 - - - -
203B LEU* 4.0 11.9 - - + +
236B GLY 4.1 0.2 - - - +
237B LEU* 3.2 3.8 - - - -
238B PHE* 3.0 65.8 + + + -
240B VAL* 4.0 2.1 - - + +
142D TYR* 3.3 27.8 + + - -
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Residues in contact with VAL 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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141B TYR* 3.9 18.6 - - + +
142B TYR* 1.3 75.5 - - - +
144B PHE* 1.3 62.7 + - - +
165B LEU* 4.1 19.7 - - + -
179B LEU* 3.8 8.4 - - + +
201B GLY* 3.1 1.7 - - - -
202B ARG 2.9 31.0 + - - +
204B LEU* 3.7 26.9 - - + -
206B LEU* 4.6 4.3 - - + -
212B LEU* 4.4 6.1 - - + -
235B LEU* 4.0 20.0 - - + -
236B GLY 3.5 10.8 - - - +
237B LEU* 3.9 19.5 - - + -
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Residues in contact with PHE 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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94B GLN* 3.6 22.0 - - - -
142B TYR* 3.9 21.8 - + + -
143B VAL* 1.3 75.2 - - - +
145B PHE* 1.3 65.5 + - - +
146B GLN* 5.3 2.0 - - + -
179B LEU* 4.1 2.7 - - - -
199B PHE* 3.6 32.3 - + + -
200B GLN 3.1 13.5 - - - +
201B GLY* 3.8 3.8 - - - -
234B VAL* 4.5 7.6 - - + -
235B LEU* 3.6 1.9 - - - +
236B GLY* 2.8 63.9 + - - +
237B LEU* 3.8 5.2 - - - -
238B PHE* 4.3 9.6 - + - -
142D TYR* 4.0 16.4 - + - -
201D GLY 4.1 1.3 - - - -
202D ARG* 4.0 16.2 - - + -
203D LEU* 4.0 10.5 - - + -
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Residues in contact with PHE 145 (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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109B TRP* 5.9 0.2 - - + -
144B PHE* 1.3 74.4 - - - +
146B GLN* 1.3 61.3 + - - +
163B LEU* 3.7 37.7 - - + -
165B LEU* 3.8 24.0 - - + -
179B LEU* 3.6 43.9 - - + +
180B ALA* 3.9 7.6 - - - -
181B LEU* 3.8 27.8 - - + +
199B PHE* 3.5 6.3 - - - -
200B GLN* 2.8 36.7 + - + +
214B VAL* 4.1 12.8 - - + -
234B VAL 3.2 13.9 - - - +
235B LEU* 4.0 17.9 - - + -
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Residues in contact with GLN 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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144B PHE* 5.5 1.8 - - + -
145B PHE* 1.3 73.8 - - - +
147B LEU* 1.3 64.8 + - - +
148B GLU* 6.3 0.4 - - + -
163B LEU* 4.1 3.4 - - - +
181B LEU* 4.8 0.4 - - - -
198B GLY 3.3 8.1 - - - +
199B PHE* 4.1 9.6 - - + +
232B ALA 3.3 18.4 + - - +
233B THR* 3.5 6.2 - - - +
234B VAL* 2.9 36.5 + - + +
200D GLN* 3.3 35.2 + - - +
201D GLY 2.8 28.6 + - - +
202D ARG* 3.1 41.5 - - - +
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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