Contacts of the strand formed by residues 219 - 226 (chain A) in PDB entry 1VE3
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 SER 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A TYR* 3.1 31.1 + - - -
142A PHE 3.4 5.8 - - - -
143A THR* 3.0 24.6 + - - +
214A LYS* 3.6 1.9 - - - +
215A VAL* 2.6 45.2 + - - -
216A GLY* 5.3 0.2 - - - -
218A TYR* 1.3 78.4 + - - +
220A TYR* 1.3 69.0 + - - +
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Residues in contact with TYR 220 (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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140A MSE 3.6 1.7 - - - +
141A TYR* 3.2 9.7 - - - -
142A PHE* 3.0 56.0 + + + -
144A ASP* 4.4 6.9 + - + -
196A LYS* 3.4 51.1 - - + +
212A GLU* 4.5 8.3 - - + -
213A GLU 3.4 3.8 - - - +
214A LYS* 3.4 51.9 + - + -
215A VAL 4.5 0.2 - - - +
218A TYR* 3.8 31.7 - - - -
219A SER* 1.3 78.9 - - - +
221A LEU* 1.3 60.3 - - - +
222A THR* 3.9 7.4 - - - +
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Residues in contact with LEU 221 (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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28A LEU* 4.5 8.5 - - + -
31A LEU* 3.4 44.6 - - + +
32A LEU* 4.2 11.7 - - + +
35A TYR* 4.4 9.4 - - + -
110A ILE* 6.2 0.9 - - + -
139A ILE* 3.8 26.5 - - + -
140A MSE 3.4 8.5 - - - +
141A TYR* 4.1 16.6 - - + -
211A ALA 4.7 0.2 - - - -
212A GLU* 3.4 2.9 - - - +
213A GLU* 2.8 53.3 + - + +
215A VAL* 4.4 10.0 - - + +
220A TYR* 1.3 71.9 - - - +
222A THR* 1.3 61.2 + - - +
223A VAL* 5.2 1.4 - - + +
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Residues in contact with THR 222 (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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138A PHE 3.6 1.4 - - - +
139A ILE* 3.4 7.2 - - - +
140A MSE 2.9 41.8 + - - -
142A PHE* 4.1 15.2 - - - -
200A GLU* 4.4 0.7 + - - -
209A LYS* 4.4 3.8 - - - -
211A ALA 3.7 10.3 - - - +
212A GLU* 2.9 26.0 + - - +
220A TYR* 4.4 1.2 - - - +
221A LEU* 1.3 76.9 - - - +
223A VAL* 1.3 67.2 + - - +
224A TYR* 3.1 46.4 + - + +
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Residues in contact with VAL 223 (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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35A TYR* 3.5 41.5 - - + -
137A LYS* 3.8 17.5 - - + -
138A PHE 3.6 2.2 - - - -
139A ILE* 4.2 19.1 - - + -
209A LYS* 3.5 4.5 - - - +
210A GLU* 2.7 62.2 + - + +
211A ALA* 2.9 23.4 + - + +
221A LEU* 5.2 3.1 - - + +
222A THR* 1.3 77.0 - - - +
224A TYR* 1.3 56.9 - - - +
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Residues in contact with TYR 224 (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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137A LYS* 3.4 2.1 - - - +
138A PHE* 2.7 67.4 + + + +
140A MSE 4.9 11.4 - - + -
142A PHE* 6.1 1.4 - + - -
199A VAL* 5.3 4.1 - - + +
200A GLU* 3.1 31.6 + - + +
203A ALA* 3.5 26.6 - - + +
204A LYS* 5.6 1.3 - - + -
207A PHE* 3.6 28.5 - - + -
208A THR 3.5 14.8 - - - -
209A LYS* 3.5 24.9 - - + -
222A THR* 3.1 32.4 + - + +
223A VAL* 1.3 72.1 - - - +
225A ASN* 1.3 71.6 + - - +
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Residues in contact with ASN 225 (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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134A PRO 5.5 2.5 - - - +
136A GLY 3.8 3.2 + - - +
137A LYS* 3.5 13.5 - - - +
207A PHE* 3.3 5.3 - - - -
208A THR* 2.9 45.4 + - - +
209A LYS 5.2 0.2 - - - -
210A GLU* 2.9 42.5 + - - +
224A TYR* 1.3 81.6 + - - +
226A PRO* 1.3 71.4 - - + +
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Residues in contact with PRO 226 (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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129A ARG* 4.0 23.1 - - + +
132A LEU* 3.8 24.7 - - + +
133A LYS 3.5 22.7 - - - +
134A PRO* 3.6 20.6 - - + +
136A GLY 3.4 17.0 - - - +
206A TYR 3.8 0.4 - - - +
207A PHE* 3.7 12.1 - - + -
208A THR* 5.4 0.7 + - - -
225A ASN* 1.3 90.1 - - + +
227A LYS* 1.3 64.6 + - - +
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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