Contacts of the strand formed by residues 207 - 215 (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 PHE 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A PHE* 3.6 34.8 - + + -
128A VAL* 3.9 9.2 - - + -
129A ARG* 4.0 19.3 - - + -
132A LEU* 4.5 2.7 - - + -
138A PHE* 3.5 41.7 - + + -
203A ALA* 2.8 34.8 + - + +
204A LYS* 3.8 10.0 - - - +
206A TYR* 1.3 90.2 - - + +
208A THR* 1.3 61.0 + - - +
224A TYR* 3.6 31.1 - + + -
225A ASN 3.3 10.8 - - - +
226A PRO* 3.7 17.3 - - + -
227A LYS* 3.4 17.1 + - - +
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Residues in contact with THR 208 (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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207A PHE* 1.3 74.7 - - - +
209A LYS* 1.3 63.6 + - - +
224A TYR* 3.5 3.3 - - - -
225A ASN* 2.9 45.5 + - - +
226A PRO 5.4 0.7 + - - +
227A LYS* 3.5 31.2 - - + +
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Residues in contact with LYS 209 (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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196A LYS* 3.9 0.6 - - - +
200A GLU* 3.4 24.8 + - - -
204A LYS* 6.0 4.5 - - - +
208A THR* 1.3 74.5 - - - +
210A GLU* 1.3 61.8 + - - +
211A ALA* 4.6 9.0 - - - +
212A GLU* 2.7 47.5 + - + +
222A THR* 4.4 3.8 - - + -
223A VAL 3.5 7.0 - - - +
224A TYR* 3.5 24.2 - - + -
225A ASN* 5.2 0.2 - - - -
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Residues in contact with GLU 210 (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* 4.3 9.8 - - + -
137A LYS* 3.0 38.5 + - - +
208A THR 3.6 2.6 + - - -
209A LYS* 1.3 75.5 - - - +
211A ALA* 1.3 63.0 + - + +
223A VAL* 2.7 25.3 + - + +
225A ASN* 2.9 42.4 + - - +
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Residues in contact with ALA 211 (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* 3.4 40.8 - - + +
209A LYS* 3.6 6.0 - - - +
210A GLU* 1.3 82.9 + - + +
212A GLU* 1.3 64.7 + - - +
222A THR* 3.7 5.0 - - - +
223A VAL* 2.9 31.8 + - + +
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Residues in contact with GLU 212 (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* 4.6 0.4 + - - -
196A LYS* 2.8 27.0 + - - -
200A GLU* 2.7 22.0 - - - +
209A LYS* 2.7 29.6 + - + +
211A ALA* 1.3 79.9 - - - +
213A GLU* 1.3 70.8 + - - +
214A LYS 4.3 0.5 + - - -
220A TYR* 4.5 13.3 - - + +
221A LEU 3.4 6.3 - - - +
222A THR* 2.9 22.3 + - - +
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Residues in contact with GLU 213 (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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31A LEU* 4.4 25.0 - - + +
34A LYS* 3.1 23.3 + - - -
35A TYR* 2.5 41.8 + - + +
212A GLU* 1.3 78.1 - - - +
214A LYS* 1.3 65.6 + - - +
215A VAL* 3.6 0.7 + - - +
220A TYR* 3.4 7.1 - - - +
221A LEU* 2.8 56.8 + - + +
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Residues in contact with LYS 214 (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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212A GLU 4.3 0.8 + - - -
213A GLU* 1.3 74.6 + - - +
215A VAL* 1.3 64.0 + - - +
216A GLY 4.2 11.0 + - - +
217A ASN 3.8 22.1 + - - -
218A TYR* 4.6 7.7 - - - -
219A SER 3.6 5.4 - - - +
220A TYR* 3.4 41.0 + - + -
38B LYS* 6.1 3.8 - - - +
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Residues in contact with VAL 215 (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 THR* 4.0 26.2 - - + -
28A LEU* 4.8 0.9 - - + -
31A LEU* 3.8 28.0 - - + -
141A TYR* 3.8 36.6 - - + +
213A GLU 3.9 10.3 - - - +
214A LYS* 1.3 76.8 - - - +
216A GLY* 1.3 67.2 + - - +
218A TYR 3.9 0.2 + - - -
219A SER* 2.6 42.5 + - - +
221A LEU* 4.4 4.3 - - + +
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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