Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 3A3K
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 GLN 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A HIS* 4.6 3.5 - - - -
148A HIS* 1.3 83.1 - - + +
150A ALA* 1.3 68.6 + - - +
181A ILE* 4.2 5.2 - - - +
182A THR* 3.4 24.4 + - - +
184A ASN* 3.2 14.7 - - - +
205A ARG 5.0 0.6 + - - -
206A LYS* 2.7 34.7 + - - +
207A GLY* 4.9 2.0 - - - -
208A ARG 6.0 0.2 - - - -
209A VAL* 4.2 6.8 + - - +
419A ASP* 3.3 36.0 + - - +
420A VAL* 4.7 3.2 - - + +
425A PHE* 3.7 29.4 - - + -
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Residues in contact with ALA 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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141A HIS* 4.2 13.2 - - + -
149A GLN* 1.3 83.1 - - - +
151A LEU* 1.3 60.3 + - - +
152A VAL* 5.6 0.2 - - + -
181A ILE* 4.0 18.6 - - + -
182A THR 3.0 7.4 + - - +
183A VAL* 3.4 9.1 - - + -
184A ASN* 3.0 25.3 + - - +
206A LYS 4.8 1.1 - - - -
207A GLY* 5.0 1.3 - - - -
209A VAL 3.4 13.0 - - - +
211A TYR* 4.3 13.9 - - + -
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Residues in contact with LEU 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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150A ALA* 1.3 74.3 - - - +
152A VAL* 1.3 71.4 + - - +
153A LEU* 4.0 28.3 - - + -
184A ASN* 3.4 25.6 - - + +
185A HIS* 4.3 4.5 - - - +
186A GLN* 4.7 2.9 - - + -
202A ALA* 3.4 29.4 - - + +
203A VAL* 3.7 9.6 - - - +
206A LYS* 4.1 18.8 - - + +
207A GLY* 4.1 1.7 - - - +
209A VAL 3.0 7.3 + - - +
210A ILE* 3.4 33.1 - - + +
211A TYR* 2.9 25.8 + - - +
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Residues in contact with VAL 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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150A ALA* 5.4 0.7 - - + -
151A LEU* 1.3 79.6 - - - +
153A LEU* 1.3 69.4 + - - +
154A TYR* 4.3 0.9 - - - -
168A VAL* 3.6 41.5 - - + -
171A LEU* 4.6 13.7 - - + -
172A TYR* 6.2 0.2 - - + -
183A VAL* 3.8 25.1 - - + -
184A ASN 2.8 12.0 + - - +
185A HIS* 3.2 5.8 - - + +
186A GLN 3.0 25.5 + - - +
211A TYR* 3.3 29.4 - - + +
241A LEU* 4.7 6.1 - - + -
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Residues in contact with LEU 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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151A LEU* 4.0 19.7 - - + -
152A VAL* 1.3 77.8 - - - +
154A TYR* 1.3 63.6 + - - +
186A GLN* 3.4 30.7 - - + +
188A PHE* 4.3 14.1 - - + -
199A LEU* 3.8 22.7 - - + +
202A ALA* 4.6 7.0 - - + -
203A VAL* 3.8 27.1 - - + -
210A ILE* 4.1 12.3 - - + -
211A TYR 2.7 12.1 + - - +
212A ILE* 3.2 19.5 - - + -
213A CYS 2.8 24.1 + - - -
222A LEU* 5.1 6.5 - - + -
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Residues in contact with TYR 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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152A VAL 4.3 3.8 - - - -
153A LEU* 1.3 78.3 - - - +
155A ALA* 1.3 63.1 + - - +
156A ASP* 4.8 1.8 - - - -
164A CYS* 4.2 2.2 - - + -
165A PHE* 3.9 51.6 - + + -
168A VAL* 3.6 42.0 - - + -
185A HIS* 4.4 15.0 + - + -
186A GLN 3.2 27.6 + - - -
187A GLU* 3.4 34.8 + - + +
188A PHE* 3.1 27.4 + - - -
213A CYS* 3.2 15.0 - - + +
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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