Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 1BFD
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU 2.9 15.4 + - - +
93A ILE* 3.9 10.5 - - + -
94A VAL* 3.0 31.2 + - - +
123A VAL* 4.3 3.4 - - - -
124A LYS* 4.2 10.3 - - + -
125A TRP* 3.3 19.7 - - + +
142A ALA* 3.4 33.0 - - + +
145A MET* 3.8 16.8 - - + -
146A ALA* 3.7 26.9 - - + +
152A GLY 4.1 0.7 - - - +
153A PRO* 1.3 80.0 - - - +
155A TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 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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75A THR* 2.9 44.1 + - + +
82A LEU* 5.9 1.1 - - + -
94A VAL* 3.3 30.1 - - + -
96A ALA* 3.4 18.2 - - + +
112A ASN* 2.9 22.3 + - - -
115A ALA 3.6 22.4 - - - -
116A ALA* 4.7 1.6 - - - -
118A LEU* 4.5 0.3 - - - +
119A PRO* 3.5 19.7 - - + -
123A VAL* 4.3 6.5 - - + -
125A TRP* 2.9 17.1 + - - +
126A SER* 3.3 26.6 - - - +
127A TYR* 3.0 26.6 + - - -
142A ALA* 5.8 0.2 - - - -
154A VAL* 1.3 77.9 - - - +
156A LEU* 1.3 63.2 + - - +
157A SER* 4.3 13.9 - - - -
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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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93A ILE* 6.0 0.4 - - + -
94A VAL 2.9 9.9 + - - +
95A THR* 3.2 11.2 - - + -
96A ALA* 3.0 25.1 + - - +
125A TRP* 4.6 4.7 - - + -
127A TYR* 3.4 23.8 - - + +
129A PRO* 4.0 12.8 - - + -
135A VAL* 4.8 2.5 - - + +
138A ALA* 3.8 24.0 - - + +
139A MET* 3.8 52.5 - - + +
142A ALA* 4.8 9.9 - - + -
155A TYR* 1.3 78.6 - - - +
157A SER* 1.3 60.6 + - - +
158A VAL* 4.0 17.1 + - + +
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Residues in contact with SER 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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96A ALA* 3.4 7.5 + - - +
97A GLY 5.0 0.3 - - - -
98A GLN* 3.5 12.8 + - - +
112A ASN* 4.6 3.6 + - - +
115A ALA* 3.8 20.5 - - - +
127A TYR 3.0 12.6 + - - -
128A GLU* 2.7 32.4 + - - +
129A PRO* 3.1 25.5 - - - +
155A TYR* 4.3 11.6 - - - -
156A LEU* 1.3 73.8 - - - +
158A VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 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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95A THR* 5.6 4.3 - - - -
96A ALA 3.0 11.9 + - - +
97A GLY* 3.6 5.6 - - - -
98A GLN* 2.9 20.5 + - - -
129A PRO* 4.8 1.3 - - + -
135A VAL* 4.0 21.1 - - + -
139A MET* 5.4 1.6 - - + -
156A LEU* 4.0 27.1 - - + +
157A SER* 1.3 80.1 + - - +
159A PRO* 1.3 78.0 - - - +
160A TYR* 3.3 2.1 + - - -
162A ASP* 3.9 14.8 - - + +
163A TRP* 3.5 40.3 + - + -
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Residues in contact with PRO 159 (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 GLN* 3.6 18.8 - - + +
99A GLN 3.4 17.9 - - - +
101A ARG* 3.7 35.0 - - + +
104A ILE* 4.1 6.1 - - + -
128A GLU* 4.4 9.4 - - + -
129A PRO* 4.8 1.6 - - + -
157A SER 4.0 5.4 - - - +
158A VAL* 1.3 87.6 - - - +
160A TYR* 1.3 65.5 + - - +
161A ASP* 3.2 14.6 - - - +
162A ASP* 3.1 35.2 + - - +
163A TRP* 4.2 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