Contacts of the strand formed by residues 84 - 88 (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 THR 84 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I PRO* 4.0 1.2 - - - +
83I ARG* 1.3 81.3 + - - +
85I ILE* 1.3 67.8 + - - +
86I VAL* 4.0 14.8 - - + -
111I GLN* 3.5 11.9 - - + +
113I ILE* 3.9 24.9 - - + -
151I MET* 3.5 13.3 - - + +
152I ALA* 2.7 36.3 + - - +
154I PRO 3.2 3.7 + - - +
155I LEU* 3.2 17.8 - - + +
156I ILE 2.9 24.1 + - - -
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Residues in contact with ILE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I LEU* 3.9 12.1 - - + -
82I PRO* 3.9 21.5 - - + -
84I THR* 1.3 78.3 - - - +
86I VAL* 1.3 64.7 + - - +
87I GLU* 5.2 0.4 - - + -
99I PHE* 3.9 51.1 - - + -
103I THR* 4.1 9.2 - - + -
110I CYS* 3.7 21.7 - - - -
111I GLN 3.1 7.8 + - - +
112I VAL* 3.3 11.5 - - + +
113I ILE* 2.9 24.1 + - - +
156I ILE* 3.4 16.4 - - + +
158I ILE* 4.3 11.0 - - + -
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Residues in contact with VAL 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I THR* 4.0 19.1 - - + -
85I ILE* 1.3 76.8 - - - +
87I GLU* 1.3 65.9 + - - +
88I LEU 4.7 1.1 - - - +
113I ILE* 3.4 18.8 - - + +
115I ILE* 3.6 32.3 - - + -
148I LEU* 4.6 9.9 - - + -
155I LEU* 4.5 12.6 - - + -
156I ILE 2.8 13.7 + - - +
157I PHE* 4.1 27.6 - - + -
158I ILE* 3.0 31.5 + - - +
176I LEU* 5.7 1.3 - - + -
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Residues in contact with GLU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LYS* 2.8 36.7 + - - -
85I ILE* 5.2 1.3 - - + -
86I VAL* 1.3 76.3 - - - +
88I LEU* 1.3 65.5 + - - +
89I GLY 3.4 11.3 + - - +
95I SER* 3.7 9.3 + - - -
96I LEU* 3.7 25.6 - - + -
99I PHE* 4.0 18.2 - - + -
112I VAL* 5.6 1.1 - - + -
113I ILE 2.7 15.4 + - - +
114I GLY* 3.3 1.4 - - - -
115I ILE 2.9 25.6 + - - -
158I ILE* 3.7 14.9 - - + +
160I ASN* 2.6 22.0 + - - -
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Residues in contact with LEU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I VAL* 4.0 1.4 - - + +
87I GLU* 1.3 70.4 + - - +
89I GLY* 1.3 60.8 + - - +
115I ILE* 3.8 27.1 - - + +
116I ASP* 5.7 0.9 - - - -
139I CYS* 3.5 27.1 - - - -
145I PHE* 3.7 31.2 - - + -
157I PHE* 4.1 18.2 - - + -
158I ILE 2.9 19.3 + - - +
159I ASP* 4.1 19.5 - - - +
160I ASN* 3.0 28.1 + - - +
161I ALA* 3.4 6.4 + - + -
168I ILE* 3.9 18.8 - - + -
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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