Contacts of the strand formed by residues 155 - 159 (chain K) in PDB entry 2BM8
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 155 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K LEU* 4.5 0.7 - - - +
84K THR* 3.2 33.7 - - + +
86K VAL* 4.4 10.1 - - + -
148K LEU* 5.6 0.7 - - + -
151K MET* 4.8 5.6 - - + -
152K ALA 4.3 5.4 - - - +
153K HIS* 3.7 9.6 - - + +
154K PRO* 1.3 75.3 - - - +
156K ILE* 1.3 81.9 + - - +
157K PHE* 3.7 16.4 - - + +
176K LEU* 4.0 30.3 - - + -
177K LEU* 4.1 16.6 - - + -
181K ASP* 3.1 24.2 + - - +
182K TYR 3.0 22.7 + - - -
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Residues in contact with ILE 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K TYR* 4.7 2.0 - - + -
76K MET* 3.7 25.6 - - + +
77K LEU* 3.7 26.0 - - + -
80K LEU* 4.0 14.4 - - + -
82K PRO* 3.9 16.4 - - + -
84K THR 2.9 7.5 + - - +
85K ILE* 3.4 12.0 - - + -
86K VAL* 2.8 28.8 + - - +
99K PHE* 6.0 0.4 - - + -
155K LEU* 1.3 80.0 - - - +
157K PHE* 1.3 61.4 + - - +
158K ILE* 3.7 26.7 - - + -
182K TYR* 3.9 9.2 - - + -
184K ILE* 3.7 21.3 - - + -
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Residues in contact with PHE 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K VAL* 3.8 30.1 - - + -
88K LEU* 4.2 21.3 - - + -
145K PHE* 4.0 32.1 - + - -
148K LEU* 4.6 2.9 - - + -
155K LEU* 3.7 8.0 - - + +
156K ILE* 1.3 72.5 - - - +
158K ILE* 1.3 69.0 + - - +
159K ASP* 4.8 0.9 - - - -
168K ILE* 4.0 13.2 - - + -
171K TRP* 5.1 2.5 - + - -
172K ALA* 5.4 1.3 - - + -
176K LEU* 3.9 27.1 - - + -
177K LEU* 4.7 2.2 - - + -
182K TYR 3.0 15.1 + - - +
183K PHE* 3.2 43.4 - + + -
184K ILE* 2.8 27.0 + - - +
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Residues in contact with ILE 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K TYR* 3.5 33.7 - - + +
85K ILE* 4.2 7.4 - - + -
86K VAL 3.0 14.3 + - - +
87K GLU* 3.5 6.2 - - - +
88K LEU* 2.8 30.5 + - - +
99K PHE* 3.6 34.8 - - + -
156K ILE* 3.7 19.3 - - + -
157K PHE* 1.3 81.9 - - - +
159K ASP* 1.3 61.5 + - - +
160K ASN* 3.4 26.8 + - - +
184K ILE* 3.4 6.5 - - + +
186K GLU* 3.7 10.8 - - + +
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Residues in contact with ASP 159 (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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88K LEU* 3.9 18.1 - - + +
157K PHE* 4.1 2.2 - - + -
158K ILE* 1.3 71.0 - - - +
160K ASN* 1.3 58.2 + - - +
161K ALA* 3.0 10.0 + - - +
162K HIS* 2.9 55.3 + - - -
163K ALA 4.7 0.3 + - - -
165K THR* 3.4 20.7 + - - +
183K PHE* 4.6 12.1 - - + -
184K ILE 2.7 15.8 + - - +
185K ILE* 4.0 13.5 - - + +
186K GLU* 3.2 24.6 + - - +
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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