Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 4K8T
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 ALA 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PHE* 3.3 20.6 - - + +
5A LEU* 4.0 23.1 - - + +
144A VAL 3.1 14.4 + - - +
145A VAL 3.2 7.1 + - - +
146A ALA 3.5 0.4 - - - -
147A ASP* 1.3 78.1 - - - +
149A LYS* 1.3 65.8 + - - +
150A VAL* 3.3 10.3 + - - +
151A THR* 4.4 3.9 + - - +
179A ARG* 3.1 25.7 - - - +
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Residues in contact with LYS 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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0A THR* 4.0 19.3 - - - +
2A PHE 3.0 12.9 + - - +
3A ASP* 3.1 33.7 + - - +
148A ALA* 1.3 72.7 - - - +
150A VAL* 1.3 64.8 + - + +
179A ARG* 3.6 12.8 - - - +
180A GLU* 3.2 24.6 + - - +
287A THR* 2.9 40.4 + - + +
288A GLN* 5.2 2.0 + - - -
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Residues in contact with VAL 150 (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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3A ASP 2.8 9.0 + - - +
4A VAL* 3.3 6.9 - - + -
5A LEU 2.7 32.6 + - - +
148A ALA* 4.0 3.6 - - - +
149A LYS* 1.3 83.3 - - + +
151A THR* 1.3 69.3 + - - +
152A TYR* 4.4 4.3 - - + +
180A GLU* 3.4 14.4 - - + +
182A SER* 3.9 19.7 - - - -
209A ILE* 5.1 2.7 - - + -
283A LEU* 4.2 15.5 - - + -
286A TYR* 4.1 23.1 - - + -
287A THR* 3.8 22.0 - - + -
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Residues in contact with THR 151 (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* 3.1 37.0 - - + +
7A VAL* 4.4 12.6 - - + -
145A VAL* 3.8 17.1 + - - +
148A ALA* 4.4 4.6 + - - +
150A VAL* 1.3 75.0 + - - +
152A TYR* 1.3 57.9 + - - +
153A PHE* 5.6 1.3 - - + -
167A ILE* 6.1 0.9 - - + -
170A CYS* 4.4 15.0 - - + -
174A ALA* 4.7 2.8 - - - +
180A GLU 3.0 7.2 + - - -
181A MSE 3.4 29.3 - - + +
182A SER 2.8 31.4 + - - +
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Residues in contact with TYR 152 (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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4A VAL* 4.4 2.0 - - + -
5A LEU 2.6 13.7 + - - +
6A THR* 3.0 24.5 - - + -
7A VAL* 2.8 26.7 + - - +
58A SER* 4.7 3.8 + - - -
59A ALA* 4.5 11.7 - - + -
62A THR* 3.8 24.3 + - + -
150A VAL* 4.6 0.4 - - + -
151A THR* 1.3 74.6 - - - +
153A PHE* 1.3 66.8 + - - +
182A SER* 3.2 28.0 - - - -
184A THR* 3.3 39.0 - - + +
211A PHE* 3.6 25.0 - + - +
275A GLY 5.0 2.9 + - - -
276A ASP* 5.0 1.6 + - - -
279A ALA* 3.6 20.3 - - + +
283A LEU* 3.7 23.1 - - + -
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Residues in contact with PHE 153 (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 VAL* 3.4 12.3 - - + +
151A THR* 5.3 1.3 - - + -
152A TYR* 1.3 79.5 - - - +
154A GLU* 1.4 71.7 + - - +
157A LEU* 4.1 0.9 - - + -
158A TRP* 3.7 25.1 - + - -
167A ILE* 3.6 37.5 - - + -
181A MSE 3.6 32.1 - - + -
182A SER 2.9 31.0 + - - -
183A MSE 3.1 29.2 - - + +
184A THR* 3.0 27.5 + - - +
201A LEU* 4.1 7.6 - - + -
207A VAL* 3.6 26.5 - - + -
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Residues in contact with GLU 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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7A VAL 3.4 9.1 + - - +
8A GLY* 3.3 14.7 - - - -
9A ASN* 3.0 26.3 + - - +
57A GLY 4.0 1.0 - - - -
58A SER* 3.2 20.4 + - - +
59A ALA* 2.8 35.3 + - + +
152A TYR* 5.6 0.4 - - + -
153A PHE* 1.4 81.8 - - - +
155A GLY* 1.3 64.2 + - - +
156A TYR* 3.6 10.3 - - + +
157A LEU* 3.0 24.2 + - + +
158A TRP* 4.4 1.4 - - - -
184A THR* 3.7 9.2 - - + -
186A SER* 3.6 7.4 - - - +
401A ADN 3.2 21.8 - - - -
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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