Contacts of the strand formed by residues 140 - 148 (chain A) in PDB entry 2DQM
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 ARG 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A THR* 2.9 26.1 + - - +
22A ASP* 2.7 44.8 + - - +
23A ILE 3.0 23.6 + - - +
139A ALA* 1.3 70.9 - - - +
141A PHE* 1.3 61.6 + - - +
142A THR* 5.0 1.8 + - - -
177A GLN* 6.2 2.0 - - - +
178A ASP 4.4 8.1 - - - +
179A PRO* 3.9 17.7 - - + +
180A PHE 4.8 0.4 - - - -
181A PRO* 3.8 30.2 - - + +
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Residues in contact with PHE 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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23A ILE* 3.5 29.4 - - + -
25A LEU* 3.9 17.7 - - + -
125A PHE* 4.1 7.4 - + - -
131A TYR* 4.3 7.4 - + - -
139A ALA* 3.3 23.1 + - + -
140A ARG* 1.3 71.9 - - - +
142A THR* 1.3 63.7 + - - +
143A THR* 4.5 5.8 - - - +
158A ASN* 6.1 0.2 - - + -
176A TRP 4.2 0.2 - - - +
177A GLN* 3.8 1.7 - - - +
178A ASP* 3.2 32.5 + - + +
180A PHE 5.2 0.2 + - - -
182A LYS* 3.7 45.4 - - + +
184A CYS* 4.0 25.8 - - + -
187A PHE* 3.7 35.4 - + + -
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Residues in contact with THR 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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23A ILE 3.1 9.2 + - - +
24A ASP* 3.5 16.6 - - - +
25A LEU* 2.8 27.9 + - - +
140A ARG 5.0 1.6 + - - -
141A PHE* 1.3 75.3 + - - +
143A THR* 1.3 63.3 + - - +
144A LYS 4.3 0.4 - - - -
162A VAL* 5.2 1.8 - - + -
175A GLN* 3.5 32.3 - - + +
176A TRP 3.2 15.0 - - - +
177A GLN* 4.1 15.7 - - + +
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Residues in contact with THR 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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25A LEU* 3.5 7.4 - - + +
27A PHE* 3.9 31.6 - - + -
141A PHE* 4.5 5.0 - - - +
142A THR* 1.3 79.9 + - - +
144A LYS* 1.3 59.5 + - - +
145A ILE* 4.1 9.6 - - + -
157A SER* 3.4 32.6 + - - +
174A VAL 3.7 1.7 - - - +
175A GLN* 3.2 4.6 - - - -
176A TRP* 2.7 42.4 + - - -
187A PHE* 3.5 17.5 - - + -
189A LEU* 4.6 0.4 - - + -
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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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24A ASP* 5.6 0.9 - - - +
25A LEU 2.7 16.0 + - - +
26A THR* 3.3 21.5 + - + +
27A PHE* 2.8 28.9 + - - +
142A THR 4.3 0.2 - - - -
143A THR* 1.3 73.2 - - - +
145A ILE* 1.3 65.0 + - - +
146A ILE* 4.4 18.6 - - + -
173A TRP* 3.9 41.2 - - + -
174A VAL 3.5 2.7 - - - -
175A GLN* 3.9 27.2 - - - +
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Residues in contact with ILE 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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27A PHE* 3.8 2.7 - - - +
29A LEU* 3.4 36.1 - - + -
143A THR* 4.1 7.6 - - + +
144A LYS* 1.3 78.2 - - - +
146A ILE* 1.3 62.5 + - - +
155A LEU* 3.5 25.0 - - + +
156A LEU 3.5 41.7 - - - +
157A SER* 4.2 4.5 - - - -
173A TRP* 3.0 25.3 - - - +
174A VAL 2.8 14.7 + - - +
176A TRP* 4.2 9.2 - - + -
189A LEU* 3.9 23.6 - - + -
190A VAL 4.8 0.2 - - - +
191A ALA* 5.2 0.2 - - + -
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Residues in contact with ILE 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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26A THR* 3.9 23.6 - - + -
27A PHE 2.8 13.3 + - - +
28A ASP* 3.8 13.2 - - + +
29A LEU* 2.8 29.2 + - - +
144A LYS* 4.4 14.8 - - + -
145A ILE* 1.3 76.9 - - - +
147A ALA* 1.3 65.9 + - - +
167A LEU* 3.5 26.7 - - + -
171A ARG* 3.2 28.9 - - + +
172A HIS 3.4 5.2 - - - +
173A TRP* 3.8 12.1 - - + -
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Residues in contact with ALA 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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29A LEU* 3.8 20.4 - - + +
145A ILE 4.3 0.2 - - - -
146A ILE* 1.3 79.0 - - - +
148A ASP* 1.3 66.6 + - - +
152A TYR* 3.8 21.3 - - + -
155A LEU* 4.0 21.9 - - + +
171A ARG* 3.3 11.5 - - - +
172A HIS* 3.0 35.0 + - - -
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Residues in contact with ASP 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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29A LEU 5.0 2.0 + - - -
147A ALA* 1.3 73.7 - - - +
149A LYS* 1.3 60.7 + - - +
150A ILE* 3.3 13.7 + - - +
151A LYS* 2.9 37.1 + - + +
152A TYR* 2.9 37.3 + - + +
169A ASN 4.6 5.0 - - - +
170A GLY* 3.8 13.8 - - - +
171A ARG* 4.3 9.8 - - + +
172A HIS* 4.3 0.2 - - - -
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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