Contacts of the helix formed by residues 1301 - 1309 (chain B) in PDB entry 1VDV
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 THR1301 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425B SER* 6.2 1.8 - - - -
504B MET* 5.5 2.7 - - + -
1207B THR 3.6 10.1 - - - +
1208B LEU 4.5 10.3 - - - +
1210B GLU* 3.7 19.9 + - + +
1299B PRO* 2.9 34.5 + - + +
1300B ALA* 1.3 72.1 - - - +
1302B PRO* 1.3 78.6 - - + +
1303B GLU* 3.1 12.5 + - - +
1304B LYS* 3.1 23.0 + - - +
1305B ILE* 2.9 25.1 + - - +
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Residues in contact with PRO1302 (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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423B GLN* 3.7 20.6 - - - +
424B ALA 3.6 13.7 - - - +
425B SER* 3.5 32.1 - - - +
507B PHE* 3.8 10.5 - - + -
1169B GLY* 3.3 27.4 - - - +
1170B ASP* 4.9 2.2 - - - +
1171B HIS* 6.1 1.6 - - - +
1207B THR 4.6 4.3 - - - +
1208B LEU* 6.1 0.7 - - + -
1301B THR* 1.3 90.8 - - + +
1303B GLU* 1.3 56.7 + - - +
1305B ILE* 5.7 0.2 - - + -
1306B ARG* 2.9 34.0 + - - +
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Residues in contact with GLU1303 (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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504B MET* 3.1 55.7 - - + +
507B PHE* 3.7 28.9 + - + +
1210B GLU* 4.5 4.9 - - - +
1212B HIS* 5.5 0.2 + - - -
1301B THR* 3.0 9.9 + - - +
1302B PRO* 1.3 80.7 - - - +
1304B LYS* 1.3 70.7 + - + +
1306B ARG* 4.0 0.3 - - - +
1307B ASN* 3.0 48.3 + - - +
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Residues in contact with LYS1304 (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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735B TYR* 6.4 0.2 - - - -
1210B GLU* 3.1 27.9 + - - -
1296B LEU* 4.1 15.8 - - + +
1297B ASP* 3.3 39.9 - - - +
1298B SER 4.4 1.5 + - - -
1299B PRO* 3.0 29.4 + - - +
1300B ALA* 4.4 1.1 - - - -
1301B THR* 3.1 18.2 + - - +
1303B GLU* 1.3 89.9 + - + +
1305B ILE* 1.3 62.3 + - - +
1307B ASN* 4.0 5.1 - - - +
1308B ALA* 3.0 26.0 + - - +
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Residues in contact with ILE1305 (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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1164B ILE* 4.4 23.1 - - + -
1165B ASP 4.9 1.6 - - - +
1169B GLY* 3.6 26.9 - - - +
1171B HIS* 4.2 12.6 - - + +
1274B ILE* 3.7 33.7 - - + -
1278B ILE* 4.0 21.5 - - + +
1300B ALA* 3.7 22.7 - - + +
1301B THR 2.9 17.7 + - - +
1302B PRO* 3.8 3.8 - - + +
1304B LYS* 1.3 77.4 - - - +
1306B ARG* 1.3 63.8 + - - +
1308B ALA* 3.3 4.5 + - - +
1309B CYS* 3.2 24.9 + - - -
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Residues in contact with ARG1306 (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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507B PHE* 3.4 27.6 - - + -
510B THR* 3.4 25.0 - - + +
511B LEU* 4.9 1.3 - - + -
514B SER* 3.0 21.2 + - - -
1166B CYS 3.0 25.6 + - - -
1167B LEU* 2.8 33.0 + - - +
1168B THR* 3.6 3.4 - - - +
1169B GLY* 4.0 6.0 - - - -
1302B PRO 2.9 21.4 + - - +
1305B ILE* 1.3 73.9 - - - +
1307B ASN* 1.3 64.9 + - - +
1309B CYS* 3.0 39.8 + - - +
1311B ASP* 2.9 24.2 + - - -
1313B PHE* 4.0 6.7 - - - +
1314B THR* 3.5 5.9 - - - +
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Residues in contact with ASN1307 (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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506B GLU* 4.1 16.7 + - - +
507B PHE* 3.6 29.5 + - - +
510B THR* 4.6 4.5 + - - -
1303B GLU* 3.0 42.5 + - - +
1304B LYS* 4.1 4.4 - - - +
1306B ARG* 1.3 78.6 - - - +
1308B ALA* 1.3 60.0 + - - +
1309B CYS 3.5 0.3 + - - -
1310B VAL* 3.8 16.8 + - - +
1314B THR* 4.8 9.0 - - - +
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Residues in contact with ALA1308 (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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1278B ILE* 3.6 26.2 - - + -
1282B ARG* 2.7 40.3 + - - +
1294B PHE* 4.7 9.2 - - + -
1295B ARG 6.0 0.7 - - - +
1296B LEU* 4.9 4.7 - - + -
1304B LYS 3.0 19.8 + - - +
1305B ILE 3.6 4.3 - - - +
1306B ARG 3.2 0.4 - - - -
1307B ASN* 1.3 73.3 - - - +
1309B CYS* 1.3 56.8 + - - +
1310B VAL 2.9 8.7 + - - -
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Residues in contact with CYS1309 (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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1164B ILE* 4.1 15.3 - - - -
1166B CYS* 3.8 27.8 - - + +
1278B ILE* 4.6 6.1 - - - -
1281B ALA* 3.8 28.3 - - + -
1282B ARG* 4.9 5.2 - - - +
1305B ILE* 3.2 18.5 + - - -
1306B ARG* 3.0 37.3 + - - +
1307B ASN 4.3 0.4 - - - -
1308B ALA* 1.3 74.8 - - - +
1310B VAL* 1.3 65.4 + - - +
1311B ASP* 3.3 6.8 + - - +
1314B THR* 3.7 0.3 - - - +
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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