Contacts of the strand formed by residues 219 - 225 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B TYR* 3.4 24.4 + - - -
142B PHE 3.6 9.9 - - - -
143B THR* 3.3 7.1 - - - +
144B ASP 3.0 20.4 + - - +
147B GLU* 2.8 15.5 + - - -
214B LYS* 3.4 4.3 - - - +
215B VAL 2.8 35.4 + - - +
218B TYR* 1.3 76.5 - - - +
220B TYR* 1.3 72.8 + - - +
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B MSE 3.9 0.9 - - - +
141B TYR* 2.9 29.4 - - - -
142B PHE* 3.8 14.0 + + + +
196B LYS* 3.3 54.4 - - + +
212B GLU* 4.0 20.4 - - + -
213B GLU 3.4 3.6 - - - -
214B LYS* 3.1 51.2 + - + -
215B VAL 4.5 0.2 - - - +
217B ASN 4.8 1.9 + - - -
218B TYR* 3.7 20.1 - - - -
219B SER* 1.3 79.8 - - - +
221B LEU* 1.3 59.8 + - - +
222B THR* 3.9 14.2 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.2 17.5 - - + -
31B LEU* 3.9 22.2 - - + +
32B LEU* 4.0 24.7 - - + -
35B TYR* 4.2 18.2 - - + -
110B ILE* 6.5 0.2 - - + -
139B ILE* 4.1 9.6 - - + -
140B MSE 3.4 9.0 - - - +
141B TYR* 3.9 13.7 - - + -
212B GLU* 3.5 2.3 - - - -
213B GLU* 2.9 45.4 + - + +
215B VAL* 4.7 5.6 - - + -
220B TYR* 1.3 73.2 - - - +
222B THR* 1.3 60.7 + - - +
223B VAL* 4.2 21.1 - - + -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PHE 3.6 1.6 - - - +
139B ILE* 3.4 6.1 - - - +
140B MSE 2.9 38.2 + - - +
200B GLU* 5.5 2.8 + - + +
209B LYS* 3.7 15.3 - - + -
211B ALA 3.5 13.9 - - - +
212B GLU* 4.3 8.1 + - + +
220B TYR* 3.9 14.2 + - - +
221B LEU* 1.3 75.8 + - - +
223B VAL* 1.3 65.7 + - - +
224B TYR* 3.3 42.4 + - + +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.6 39.7 - - + -
137B LYS* 3.8 18.8 - - + -
138B PHE 3.5 2.5 - - - -
139B ILE* 4.4 14.4 - - + -
209B LYS* 3.7 4.2 - - - +
210B GLU* 2.7 58.8 + - - +
211B ALA* 3.1 24.2 + - + +
221B LEU* 4.2 8.5 - - + -
222B THR* 1.3 77.2 - - - +
224B TYR* 1.3 59.0 + - - +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS* 3.5 2.4 - - - +
138B PHE* 2.7 61.0 + + + +
140B MSE 4.8 11.4 - - + -
199B VAL* 5.1 2.4 - - + +
200B GLU* 3.3 30.0 + - - +
203B ALA* 3.5 27.7 - - + +
204B LYS* 4.6 9.4 - - + -
207B PHE* 3.6 27.1 - + + -
208B THR 3.4 14.6 - - - -
209B LYS* 3.4 25.5 - - + +
222B THR* 3.3 31.6 - - + +
223B VAL* 1.3 73.3 - - - +
225B ASN* 1.3 71.1 + - - +
226B PRO* 4.3 0.7 - - - -
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Residues in contact with ASN 225 (chain B).
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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134B PRO 5.7 2.2 - - - +
135B SER 5.4 0.4 + - - -
136B GLY 3.7 7.2 + - - +
137B LYS* 3.6 11.1 - - - +
207B PHE* 3.1 4.5 - - - -
208B THR* 2.6 53.2 + - - +
210B GLU* 3.0 42.1 + - - +
224B TYR* 1.3 78.4 + - - +
226B PRO* 1.3 70.7 - - + +
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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