Contacts of the strand formed by residues 108 - 112 (chain B) in PDB entry 4BL5
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 LYS 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B THR 3.5 2.8 + - - -
65B HIS* 3.5 25.6 - - + +
66B VAL 3.1 21.4 + - - -
106B ALA* 3.3 3.9 - - - +
107B ARG* 1.3 81.1 - - + +
109B VAL* 1.3 77.1 + - - +
110B VAL* 4.2 14.6 - - + -
164B THR* 3.4 28.7 - - + +
165B PHE* 4.4 0.7 - - - -
166B THR* 4.6 5.4 - - - -
230B VAL 3.0 21.0 + - - -
231B LEU* 3.2 19.4 + - - +
232B ARG 4.5 3.6 + - - -
234B TYR 2.4 35.0 + - - +
235B ASN* 4.6 0.8 - - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.4 21.3 - - + +
68B HIS* 4.7 3.8 - - + -
97B VAL* 5.4 1.8 - - + -
98B LEU* 3.8 15.0 - - + -
101B ALA* 3.7 24.5 - - + -
106B ALA* 4.5 1.3 - - + -
108B LYS* 1.3 80.3 - - - +
110B VAL* 1.3 66.8 + - - +
111B SER* 3.5 20.9 - - - +
164B THR 3.4 4.9 + - - +
165B PHE* 3.2 36.3 - - + -
166B THR* 2.8 29.8 + - - +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL 2.9 13.1 + - - +
67B ILE* 3.5 6.4 - - + -
68B HIS 3.0 22.2 + - - +
108B LYS* 4.2 17.0 - - + -
109B VAL* 1.3 75.7 - - - +
111B SER* 1.3 66.1 + - - +
166B THR* 3.5 16.4 - - + -
167B ALA* 4.3 3.1 - - - -
168B VAL* 4.1 11.9 - - + +
227B PHE* 3.6 28.7 - - + -
230B VAL* 3.8 27.6 - - + -
231B LEU* 4.4 13.5 - - + -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 3.8 22.8 - - - +
98B LEU* 3.9 13.0 - - - +
109B VAL* 3.5 19.1 - - - +
110B VAL* 1.3 77.1 - - - +
112B CYS* 1.3 62.2 - - - +
150B ILE* 3.7 27.0 - - - +
154B ASN* 4.4 0.9 + - - -
166B THR 3.0 12.2 + - - -
167B ALA* 3.1 3.8 - - - -
168B VAL* 3.1 25.1 + - - +
227B PHE* 5.1 0.4 - - - -
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Residues in contact with CYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.5 7.0 - - - -
68B HIS* 3.5 17.6 + - - +
69B LEU* 4.5 12.3 - - + +
111B SER* 1.3 77.2 - - - +
113B LEU* 1.3 64.2 + - - +
147B LYS* 2.6 39.7 + - - +
150B ILE* 4.5 2.5 - - - +
168B VAL* 3.8 2.2 - - - -
170B PRO* 3.9 27.6 - - - -
227B PHE* 4.0 24.7 - - + -
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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