Contacts of the strand formed by residues 111 - 116 (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 GLN 111 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K ARG 2.9 12.4 + - - +
84K THR* 3.3 9.9 - - - +
85K ILE 3.1 23.2 + - - +
109K ASP* 4.1 16.3 + - - +
110K CYS* 1.3 73.7 - - - +
112K VAL* 1.3 62.1 + - - +
113K ILE* 4.2 11.4 - - + -
131K ASN* 3.4 40.7 + - - +
133K THR* 5.2 5.4 + - - +
151K MET* 5.2 11.9 - - + -
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Residues in contact with VAL 112 (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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85K ILE* 3.4 20.6 - - + +
87K GLU* 5.9 0.4 - - + -
96K LEU* 3.8 41.5 - - + +
99K PHE* 4.1 13.5 - - + +
100K ARG* 3.7 36.6 - - + +
110K CYS* 4.7 5.8 - - - +
111K GLN* 1.3 77.0 - - - +
113K ILE* 1.3 64.4 + - - +
114K GLY 4.3 0.2 - - - -
131K ASN 2.9 12.9 + - - +
132K ILE* 3.3 9.9 - - + +
133K THR* 3.1 24.1 + - - +
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Residues in contact with ILE 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K THR* 3.9 16.8 - - + -
85K ILE 2.9 9.2 + - - +
86K VAL* 3.3 6.0 - - + -
87K GLU* 2.8 28.9 + - - +
96K LEU* 4.5 0.9 - - - +
111K GLN* 4.9 4.5 - - + +
112K VAL* 1.3 85.3 - - - +
114K GLY* 1.3 62.0 + - - +
115K ILE* 4.2 16.4 - - + -
133K THR* 3.4 13.7 - - - +
135K HIS* 3.9 23.1 - - + +
147K HIS* 4.6 0.2 - - - +
148K LEU* 3.7 26.9 - - + -
151K MET* 3.4 39.0 - - + -
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Residues in contact with GLY 114 (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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87K GLU 3.6 5.2 - - - -
90K VAL* 3.6 19.2 - - - +
96K LEU* 4.3 12.2 - - - +
113K ILE* 1.3 73.0 - - - +
115K ILE* 1.3 62.7 + - - +
119K LEU* 4.7 0.2 - - - +
132K ILE* 5.5 0.2 - - - +
133K THR 2.9 9.8 + - - +
134K LEU* 3.4 8.9 - - - +
135K HIS* 2.8 28.1 + - - +
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Residues in contact with ILE 115 (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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86K VAL* 4.0 14.1 - - + -
87K GLU 3.0 12.5 + - - +
88K LEU* 3.9 19.4 - - + +
89K GLY* 2.8 27.5 + - - -
90K VAL* 3.6 2.8 - - - +
113K ILE* 4.2 11.4 - - + -
114K GLY* 1.3 77.8 - - - +
116K ASP* 1.3 67.4 + - - +
135K HIS* 3.5 16.4 - - + +
137K GLY* 4.4 17.9 - - - -
138K ASP 6.4 0.2 - - - -
144K THR* 4.6 9.0 - - + -
145K PHE* 4.0 17.5 - - + -
147K HIS* 4.2 10.5 - - + +
148K LEU* 4.0 27.6 - - + -
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Residues in contact with ASP 116 (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* 5.5 2.0 - - - -
89K GLY* 3.4 8.9 - - - -
90K VAL* 3.0 26.3 + - + +
91K TYR 4.1 4.9 + - - -
115K ILE* 1.3 78.8 - - - +
117K ARG* 1.3 80.3 + - - +
118K ASP* 3.0 30.7 + - - +
119K LEU* 4.0 13.7 - - + +
121K ARG* 4.5 6.0 + - - -
135K HIS 3.1 11.7 + - - +
136K GLN* 3.5 5.9 + - - -
137K GLY 3.2 19.2 + - - -
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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