Contacts of the strand formed by residues 108 - 112 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR 3.5 2.0 + - - -
65A HIS* 3.3 22.5 - - + +
66A VAL* 2.9 25.5 + - - +
106A ALA* 3.4 3.5 + - - +
107A ARG* 1.3 81.8 - - - +
109A VAL* 1.3 68.9 + - - +
110A VAL* 3.9 20.9 - - + -
164A THR* 3.3 31.4 - - + +
165A PHE* 4.7 1.8 - - - -
166A THR* 4.5 5.2 - - - -
230A VAL 3.1 19.7 + - - -
231A LEU 3.4 17.3 + - - +
232A ARG 4.6 0.8 - - - -
233A GLU 4.4 1.6 - - - +
234A TYR 2.5 34.4 + - - +
235A ASN* 3.6 10.1 + - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.4 24.2 - - + -
68A HIS* 4.5 2.9 - - + -
97A VAL* 5.5 1.1 - - + -
98A LEU* 3.5 24.7 - - + -
101A ALA* 3.5 32.8 - - + -
106A ALA* 4.8 1.3 - - + -
108A LYS* 1.3 79.3 - - - +
110A VAL* 1.3 62.3 + - - +
111A SER* 3.8 11.7 - - - +
164A THR 3.4 4.0 + - - -
165A PHE* 3.4 27.6 - - + -
166A THR* 2.8 35.5 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL 2.8 15.0 + - - +
67A ILE* 3.4 6.0 - - + -
68A HIS 2.9 23.3 + - - -
108A LYS* 3.9 21.1 - - + -
109A VAL* 1.3 75.0 - - - +
111A SER* 1.3 71.8 + - - +
166A THR* 3.5 16.6 - - + -
167A ALA* 4.1 7.6 - - - -
168A VAL* 3.8 13.0 - - + -
227A PHE* 4.0 15.7 - - + -
230A VAL* 3.8 27.6 - - + -
231A LEU* 4.4 12.6 - - + -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS* 3.3 37.8 - - - +
98A LEU* 3.9 8.7 - - - +
109A VAL* 3.8 10.4 - - - +
110A VAL* 1.3 75.4 - - - +
112A CYS* 1.3 62.7 + - - +
150A ILE* 3.7 28.6 - - - +
154A ASN* 4.8 0.4 + - - -
166A THR 3.0 12.0 + - - -
167A ALA* 3.2 4.4 - - - -
168A VAL* 2.8 27.9 + - - +
227A PHE* 4.3 0.8 - - - -
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Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 5.4 7.6 - - - -
68A HIS 3.6 15.0 + - - +
69A LEU* 4.2 13.5 - - + +
111A SER* 1.3 80.5 - - - +
113A LEU* 1.3 64.9 + - - +
147A LYS* 2.8 36.8 + - - +
150A ILE* 4.2 1.6 - - - +
168A VAL* 3.4 3.4 - - - -
170A PRO* 3.9 25.8 - - - -
227A PHE* 3.9 23.3 - - + -
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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