Contacts of the strand formed by residues 140 - 144 (chain A) in PDB entry 3DB4
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 TYR 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASN 4.2 3.8 - - - -
139A GLU* 1.3 84.9 - - - +
141A VAL* 1.3 64.7 + - - +
154A ALA 3.5 1.6 - - - -
155A GLN* 3.6 44.3 + - + +
189A ASP* 4.0 15.0 - - - -
206A ALA* 5.1 0.2 - - - -
207A ARG* 3.7 41.9 + - + +
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Residues in contact with VAL 141 (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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135A TYR* 4.3 18.8 - - + -
139A GLU* 4.1 4.7 - - + +
140A TYR* 1.3 79.7 - - - +
142A ASP* 1.3 66.5 + - - +
143A ALA* 5.2 0.2 - - + -
154A ALA* 2.7 45.8 + - + +
156A VAL* 4.0 28.0 - - + -
186A VAL* 4.4 9.4 - - + -
204A VAL* 4.0 24.2 - - + -
205A ARG 3.3 16.2 - - - +
206A ALA* 4.8 1.3 - - - -
207A ARG* 3.0 20.9 + - - +
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Residues in contact with ASP 142 (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 VAL* 1.3 80.2 - - - +
143A ALA* 1.3 60.5 + - - +
151A TRP* 3.4 27.8 - - + -
152A PHE* 3.4 5.6 - - - +
153A GLU* 3.7 19.6 + - - +
204A VAL* 3.4 5.0 - - - +
205A ARG* 3.0 38.3 + - + +
206A ALA 4.0 1.2 - - - +
207A ARG* 3.4 14.5 - - - +
208A ALA* 2.9 33.8 + - - +
224A MSE 4.6 8.4 - - - +
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Residues in contact with ALA 143 (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 VAL* 5.2 0.2 - - + -
142A ASP* 1.3 74.1 - - - +
144A ARG* 1.3 62.0 + - - +
145A ASP 3.4 3.3 + - - -
151A TRP* 3.6 3.4 - - - -
152A PHE* 2.8 35.1 + - - +
154A ALA* 3.9 22.4 - - + +
186A VAL* 4.1 13.0 - - + -
188A TYR* 4.1 10.1 - - + +
199A MSE 3.6 18.2 - - + -
203A ASP 3.4 4.0 - - - -
204A VAL* 4.6 3.8 - - + +
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Residues in contact with ARG 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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143A ALA* 1.3 70.6 - - - +
145A ASP* 1.3 62.5 + - - +
146A THR* 3.0 43.5 + - - +
149A GLY* 3.8 36.1 + - - +
150A ALA 3.4 5.8 - - - +
151A TRP* 3.5 35.4 - - + +
188A TYR* 4.7 0.9 - - - -
199A MSE 3.3 17.3 - - - +
202A ARG* 6.0 1.2 - - - +
203A ASP* 2.7 48.6 + - - +
260A VAL* 5.2 5.4 - - - +
261A LEU 4.0 12.5 + - - -
263A ASP* 4.4 19.9 + - - +
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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