Contacts of the strand formed by residues 143 - 149 (chain A) in PDB entry 5B6N
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.9 21.3 - - + +
6A LEU* 3.4 35.4 - - - +
7A LEU* 3.5 17.3 - - + +
8A GLY* 3.1 16.3 + - - -
9A ASP* 3.0 14.3 + - + +
135A PHE* 3.7 15.3 - - + -
136A VAL 3.4 19.1 - - - +
137A PHE* 3.5 23.3 - - + -
142A LYS* 1.3 72.4 - - - +
144A LYS* 1.3 65.7 + - - +
145A LEU 3.7 13.5 - - - +
146A SER* 4.2 16.6 - - - +
119B PRO* 5.0 1.6 - - - +
148B LEU* 5.9 0.9 - - + -
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Residues in contact with LYS 144 (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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7A LEU* 3.5 12.6 - - - +
8A GLY* 5.4 2.6 - - - -
33A TRP* 4.0 21.8 - - + -
136A VAL* 2.9 15.6 + - + +
138A GLY* 4.1 5.2 - - - +
140A ASP* 3.5 25.9 + - - -
142A LYS* 3.4 23.6 + - - +
143A LEU* 1.3 80.0 + - - +
145A LEU* 1.3 61.1 + - - +
167A LEU* 4.3 25.4 - - + -
119B PRO* 5.6 8.1 - - + +
150B PRO* 3.1 29.9 - - + +
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Residues in contact with LEU 145 (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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7A LEU* 4.1 1.5 - - - +
134A VAL* 5.8 1.8 - - + +
136A VAL* 2.8 55.5 + - + +
143A LEU* 3.7 5.4 - - - +
144A LYS* 1.3 81.3 - - - +
146A SER* 1.3 63.3 + - - +
147A ILE* 4.2 24.2 - - + +
160A ILE* 6.4 2.0 - - + -
163A VAL* 3.9 25.4 - - + -
167A LEU* 4.2 7.9 - - + -
148B LEU 3.4 14.8 - - - +
149B TYR* 3.5 37.0 - - + -
150B PRO* 3.6 13.2 - - + -
153B THR* 4.7 1.3 - - + -
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Residues in contact with SER 146 (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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5A LEU 5.5 1.6 + - - -
134A VAL 3.2 12.6 - - - -
135A PHE* 4.0 21.0 - - - -
143A LEU* 4.2 10.4 - - - +
145A LEU* 1.3 77.1 - - - +
147A ILE* 1.3 65.6 + - - +
148A LEU* 4.8 9.5 - - - +
146B SER 5.1 0.2 - - - -
147B ILE* 3.5 0.3 - - - -
148B LEU* 2.6 61.4 + - - +
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Residues in contact with ILE 147 (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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132A ARG 4.5 0.2 - - - +
133A VAL* 3.4 3.6 - - - -
134A VAL* 2.9 62.4 + - + +
145A LEU* 4.2 10.7 - - + +
146A SER* 1.3 79.2 - - - +
148A LEU* 1.3 65.3 + - - +
149A TYR* 3.3 35.7 - - + +
155A ARG* 3.7 13.9 - - + -
160A ILE* 4.6 10.3 - - + -
146B SER 3.7 3.8 - - - -
147B ILE* 3.5 23.3 - - + -
149B TYR* 4.0 16.8 - - + +
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Residues in contact with LEU 148 (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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114A LEU 6.1 0.2 - - - +
115A GLY 4.1 18.8 - - - +
116A MET 6.2 0.2 - - - -
132A ARG 3.8 2.0 - - - -
133A VAL* 3.6 25.6 - - + -
135A PHE* 5.5 3.8 - - + -
146A SER* 4.8 11.9 - - - +
147A ILE* 1.3 79.3 - - - +
149A TYR* 1.3 62.6 + - - +
5B LEU 4.8 9.6 - - - +
6B LEU* 5.0 1.8 - - + -
7B LEU* 3.6 37.9 - - + +
143B LEU* 5.4 0.2 - - + -
145B LEU* 3.3 12.0 - - - +
146B SER* 2.8 48.9 + - - +
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Residues in contact with TYR 149 (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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131A ALA* 3.6 7.8 - - - +
132A ARG* 2.8 46.6 + - + +
147A ILE* 3.3 43.4 - - + +
148A LEU* 1.3 81.3 - - - +
150A PRO* 1.3 63.4 - - + +
153A THR* 3.6 25.6 - - + +
155A ARG* 4.1 13.9 - - + -
156A ASN 5.6 0.4 - - - -
7B LEU* 3.8 4.8 - - - +
145B LEU* 3.5 20.4 - - + +
147B ILE* 4.4 13.2 - - + +
159B GLU* 3.5 28.2 + - - +
162B ARG* 4.5 3.4 - - - -
163B VAL* 3.4 25.1 - - + +
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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