Contacts of the strand formed by residues 145 - 156 (chain A) in PDB entry 2DVL
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 GLY 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ARG* 3.9 7.0 + - - +
142A VAL* 3.3 20.0 + - - +
143A LYS 3.1 4.2 - - - -
144A GLY* 1.3 81.2 - - - +
146A PHE* 1.3 79.0 + - - -
211A PHE* 3.8 7.6 - - - -
212A VAL 3.4 11.0 - - - -
214A GLU* 3.7 11.5 + - - -
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Residues in contact with PHE 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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139A ALA 4.8 1.3 - - - -
140A ARG 3.4 17.7 - - - -
141A ARG* 3.3 36.8 - - + -
142A VAL* 3.5 3.1 - - - +
145A GLY* 1.3 87.1 - - - -
147A VAL* 1.3 64.2 + - - +
148A LEU* 4.2 6.1 - - + -
170A THR* 4.3 6.7 - - + -
177A PHE* 3.7 40.6 - + + -
211A PHE* 3.3 8.3 - - - -
212A VAL* 2.8 43.5 + - + +
213A PRO 4.8 2.2 - - - -
214A GLU* 4.2 15.7 - - - -
217A LEU* 4.2 21.8 - - + -
221A GLU* 3.2 28.0 - - - -
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Residues in contact with VAL 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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138A GLU 3.6 2.3 - - - +
140A ARG* 3.0 56.5 + - + +
142A VAL* 3.5 31.9 - - + -
143A LYS* 4.5 6.5 - - - +
146A PHE* 1.3 78.8 - - - +
148A LEU* 1.3 63.4 + - - +
149A ASN* 4.2 2.3 + - - +
209A GLU* 3.0 45.1 - - - +
210A VAL 3.2 5.8 - - - +
211A PHE* 4.5 7.4 - - + -
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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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138A GLU 3.0 6.7 - - - +
139A ALA* 3.2 34.3 - - + -
146A PHE* 4.7 6.1 - - + -
147A VAL* 1.3 73.0 - - - +
149A ASN* 1.3 71.8 + - - +
166A VAL* 4.6 6.3 - - + -
168A ALA* 4.1 5.2 - - + -
177A PHE* 3.7 32.8 - - + -
179A VAL* 4.2 5.6 - - + -
207A LEU* 3.4 34.4 - - + +
209A GLU 3.3 1.6 + - - -
210A VAL* 2.8 36.9 + - + +
212A VAL* 3.9 25.4 - - + -
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Residues in contact with ASN 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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136A ARG 4.4 0.7 - - - +
137A ALA* 3.6 1.9 - - - +
138A GLU* 2.7 53.7 + - + +
140A ARG* 3.7 14.1 - - - +
147A VAL* 4.2 2.4 + - - +
148A LEU* 1.3 81.1 + - - +
150A GLY* 1.3 59.1 + - - +
207A LEU* 3.0 9.4 - - - +
208A GLU* 3.5 5.4 - - - +
209A GLU* 2.6 56.7 + - - +
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Residues in contact with GLY 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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136A ARG 5.4 1.6 - - - -
137A ALA* 4.5 10.3 - - - -
149A ASN* 1.3 76.4 - - - +
151A VAL* 1.3 69.6 + - - +
152A LYS* 5.3 0.4 - - - -
206A ARG* 3.9 0.7 - - - -
207A LEU* 3.0 38.8 + - - +
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Residues in contact with VAL 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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125A GLU* 3.2 29.8 - - - +
126A PRO* 3.9 20.7 - - + +
150A GLY* 1.3 80.8 - - - +
152A LYS* 1.3 71.3 + - - +
204A GLU* 3.6 37.0 - - + +
205A VAL 3.6 5.6 - - - +
206A ARG* 4.8 9.2 - - + -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.4 41.3 - - + -
123A LEU* 2.9 30.0 + - - +
124A THR 3.2 5.8 - - - +
125A GLU* 2.7 25.0 + - - +
135A LEU* 4.5 3.0 - - - +
137A ALA* 4.2 9.4 - - + -
151A VAL* 1.3 87.4 - - - +
153A SER* 1.3 60.2 + - - +
155A ILE* 4.0 9.0 - - + +
166A VAL* 4.4 4.9 - - + -
167A MET* 3.0 23.7 + - - +
204A GLU* 3.4 5.4 - - - +
205A VAL* 2.8 40.9 + - + +
207A LEU* 4.0 13.7 - - + -
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Residues in contact with SER 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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124A THR* 2.8 26.8 + - - +
125A GLU* 3.1 29.3 + - - +
126A PRO* 3.3 12.5 - - - +
152A LYS* 1.3 74.8 - - - +
154A TRP* 1.3 83.5 + - - +
155A ILE* 3.2 7.2 + - - +
192A GLU* 5.8 1.8 - - - -
203A ALA 4.5 1.8 - - - -
204A GLU* 4.5 13.5 - - - +
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Residues in contact with TRP 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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124A THR* 4.2 9.9 - - + -
153A SER* 1.3 88.5 - - - +
155A ILE* 1.3 55.0 + - - +
156A THR 3.4 0.2 + - - -
192A GLU* 4.2 24.3 + - + +
193A GLU 5.8 1.1 - - - -
194A LYS* 3.8 32.3 - - + -
202A THR* 3.8 20.0 - - - -
203A ALA* 3.9 7.9 + - - +
1001A FAD 2.6 101.6 + + + +
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 4.0 11.7 - - + -
121A PHE 4.2 3.8 - - - +
122A CYS* 3.5 44.6 - - + -
123A LEU 4.2 0.9 - - - +
124A THR 4.6 0.4 - - - +
152A LYS* 4.0 15.9 - - + +
153A SER 3.5 15.3 - - - +
154A TRP* 1.3 74.8 - - - +
156A THR* 1.3 73.5 + - - +
158A ALA* 3.2 12.8 + - + +
164A TYR* 4.8 0.4 - - + -
202A THR* 3.3 2.4 - - - -
203A ALA 3.1 33.2 + - - +
205A VAL* 3.5 25.6 - - + -
1001A FAD 3.7 15.7 - - + +
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Residues in contact with THR 156 (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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83A VAL* 4.3 16.4 - - + +
84A ILE* 4.5 12.6 - - + -
87A VAL* 4.2 31.2 - - + +
120A ALA* 3.6 18.2 - - - +
154A TRP 3.4 1.0 + - - -
155A ILE* 1.3 70.7 - - - +
157A SER* 1.3 77.4 + - - +
158A ALA 3.2 1.3 + - - -
200A ALA* 5.2 3.4 - - + -
201A HIS 4.5 3.6 - - - +
202A THR* 3.6 11.9 - - + +
1001A FAD 3.0 44.1 + - - +
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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