Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 4BR6
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA* 4.2 11.2 - - + -
131A LYS 3.5 20.2 - - - +
132A ASP* 4.1 11.9 - - + +
137A ASN 5.2 0.9 - - - +
139A ALA* 5.1 9.9 - - + -
141A VAL* 3.9 28.5 - - + -
143A ARG* 4.1 17.0 - - - +
149A VAL* 3.7 18.9 - - + +
150A THR* 3.5 26.1 + - - +
151A GLY 3.2 2.1 - - - +
152A GLN* 1.3 84.7 - - + +
154A VAL* 1.3 61.9 + - - +
155A PRO* 3.9 0.9 - - - +
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Residues in contact with VAL 154 (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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130A ALA* 3.2 3.8 - - - -
131A LYS* 2.9 50.4 + - + +
133A LYS* 3.9 28.7 - - + -
151A GLY 5.2 2.0 - - - +
153A LEU* 1.3 75.9 - - - +
155A PRO* 1.3 79.5 - - + +
156A LEU* 3.7 10.5 - - + +
193A ARG* 4.8 6.1 - - + +
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Residues in contact with PRO 155 (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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72A LEU* 5.8 2.7 - - + -
76A LEU* 3.6 22.4 - - + +
128A TRP* 3.6 28.7 - - + -
129A LEU 4.1 4.0 - - - +
130A ALA* 4.3 2.2 - - + -
149A VAL* 3.5 43.0 - - + +
153A LEU 3.9 0.4 - - - +
154A VAL* 1.3 93.9 - - + +
156A LEU* 1.3 64.6 + - - +
193A ARG* 3.9 11.1 - - - +
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Residues in contact with LEU 156 (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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96A LEU* 4.9 2.0 - - + -
129A LEU* 2.8 21.9 + - + +
130A ALA 3.9 2.5 - - - -
131A LYS* 3.8 24.5 - - + +
138A LEU* 3.7 31.2 - - + -
154A VAL* 3.7 9.4 - - + +
155A PRO* 1.3 81.3 - - - +
157A MET* 1.3 63.6 + - - +
190A VAL* 3.3 25.5 - - + +
193A ARG* 2.9 40.5 + - - +
194A PHE* 3.6 39.3 - - + +
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Residues in contact with MET 157 (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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80A ASN* 3.7 10.8 - - - -
110A PHE* 4.4 4.9 - - + -
114A MET* 3.6 32.8 - - + +
127A ALA 3.9 0.3 - - - +
128A TRP* 3.3 8.5 - - - -
129A LEU* 3.0 33.8 + - + -
156A LEU* 1.3 81.1 - - - +
158A GLY* 1.3 63.9 + - - +
159A ILE* 3.7 27.8 - - + -
182A TRP* 4.0 14.4 - - + -
185A ILE* 3.7 26.0 - - + -
187A TRP* 4.1 12.8 - - + -
190A VAL* 3.6 26.9 - - + -
193A ARG* 4.2 0.4 - - - +
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Residues in contact with GLY 158 (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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77A PHE* 3.2 22.0 - - - -
80A ASN* 3.1 20.7 + - - -
126A TRP* 4.2 1.1 - - - -
127A ALA 3.5 3.6 - - - -
128A TRP* 3.2 32.6 - - - -
157A MET* 1.3 72.4 - - - +
159A ILE* 1.3 68.0 + - - +
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Residues in contact with ILE 159 (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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77A PHE* 3.8 2.2 - - + -
80A ASN* 5.6 0.2 - - - +
114A MET* 4.0 9.2 - - + -
118A LEU* 3.6 33.9 - - + +
126A TRP* 3.4 6.0 - - - -
127A ALA 3.0 31.4 + - - -
157A MET* 3.7 27.1 - - + -
158A GLY* 1.3 79.5 - - - +
160A ASP* 1.3 67.5 + - - +
161A ALA 3.6 0.5 + - - -
177A TYR* 3.9 20.4 - - + +
178A PHE* 4.6 0.4 - - + -
181A ILE* 3.8 36.6 - - + -
182A TRP* 4.2 9.9 - - + -
185A ILE* 4.0 9.2 - - + -
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Residues in contact with ASP 160 (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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26A HIS* 3.0 12.3 - - - -
77A PHE* 3.7 16.4 - - + -
126A TRP* 3.3 31.7 - - + -
159A ILE* 1.3 73.5 - - - +
161A ALA* 1.3 58.7 + - - +
162A TRP* 3.0 31.1 + - - -
165A ALA* 3.5 12.5 - - + +
177A TYR* 2.9 30.7 + - - -
301A MN3 2.2 33.4 + - - -
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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