Contacts of the strand formed by residues 155 - 159 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I LEU* 4.4 1.6 - - - +
82I PRO* 4.9 0.2 - - - -
84I THR* 3.2 32.1 - - + +
86I VAL* 4.5 9.6 - - + -
151I MET* 4.9 4.7 - - + +
152I ALA 4.3 6.5 - - - +
153I HIS* 4.3 8.5 - - + +
154I PRO* 1.3 75.5 - - - +
156I ILE* 1.3 69.9 + - - +
157I PHE* 3.7 28.7 - - + +
176I LEU* 3.8 29.2 - - + -
177I LEU* 4.2 15.7 - - + -
181I ASP* 3.0 24.4 + - - +
182I TYR 3.1 22.0 + - - -
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Residues in contact with ILE 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 4.6 2.0 - - + -
76I MET* 4.0 17.5 - - + -
77I LEU* 3.8 20.0 - - + -
80I LEU* 3.9 16.6 - - + -
82I PRO* 3.7 27.1 - - + -
84I THR 2.9 8.5 + - - +
85I ILE* 3.4 12.5 - - + +
86I VAL 2.8 31.9 + - - +
99I PHE* 6.2 0.7 - - + -
155I LEU* 1.3 78.8 - - - +
157I PHE* 1.3 55.8 + - - +
158I ILE* 3.8 25.8 - - + -
182I TYR* 3.9 13.0 - - + -
184I ILE* 4.0 19.3 - - + -
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Residues in contact with PHE 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I VAL* 3.7 27.6 - - + -
88I LEU* 4.1 21.1 - - + -
145I PHE* 3.7 35.7 - + - -
148I LEU* 5.9 2.0 - - + -
155I LEU* 3.7 9.6 - - + +
156I ILE* 1.3 71.8 - - - +
158I ILE* 1.3 67.7 + - - +
159I ASP* 4.7 1.1 - - + -
168I ILE* 3.9 13.5 - - + -
171I TRP* 4.9 2.9 - + - -
172I ALA* 5.5 0.7 - - + -
176I LEU* 3.9 26.0 - - + -
177I LEU* 4.7 2.9 - - + -
182I TYR 2.9 14.3 + - - +
183I PHE* 3.3 42.0 - + + -
184I ILE* 2.8 25.8 + - - +
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Residues in contact with ILE 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I TYR* 3.5 32.5 - - + +
85I ILE* 4.3 6.3 - - + -
86I VAL 3.0 10.0 + - - +
87I GLU* 3.7 20.3 - - + +
88I LEU* 2.9 29.6 + - - +
99I PHE* 3.5 35.4 - - + -
156I ILE* 3.8 17.9 - - + -
157I PHE* 1.3 82.2 - - - +
159I ASP* 1.3 62.4 + - - +
160I ASN* 3.6 3.5 + - - +
184I ILE* 3.3 12.1 - - + +
186I GLU* 3.6 21.8 - - + +
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Residues in contact with ASP 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 4.1 16.0 - - + +
157I PHE* 4.2 2.9 + - + -
158I ILE* 1.3 71.4 - - - +
160I ASN* 1.3 58.3 + - - +
161I ALA* 3.0 11.1 + - - +
162I HIS* 2.9 42.2 + - - -
163I ALA 4.8 0.7 + - - +
165I THR* 3.2 30.4 + - - +
168I ILE* 5.8 0.3 - - - +
183I PHE* 4.6 11.2 - - + -
184I ILE 2.7 14.3 + - - +
185I ILE* 3.8 15.8 - - + +
186I GLU* 3.2 26.5 + - - +
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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