Contacts of the helix formed by residues 1392 - 1399 (chain B) in PDB entry 6V65
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 PHE1392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1289B PHE* 3.2 49.6 - + + -
1290B LYS* 4.8 2.5 - - - -
1293B GLY* 3.4 33.4 - - - -
1294B ALA* 5.3 0.7 - - - -
1296B TYR* 4.0 13.9 - + - -
1297B LEU* 3.3 37.2 - - + +
1361B LEU* 4.3 9.4 - - + -
1388B MET* 3.2 29.0 + - + +
1390B LEU 3.5 1.2 - - - -
1391B ARG* 1.3 80.6 - - - +
1393B ILE* 1.3 95.0 + - + +
1394B ASN 3.6 0.2 - - - -
1395B PRO* 3.8 6.4 - - - +
1396B ALA* 3.9 5.7 + - - +
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Residues in contact with ILE1393 (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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1296B TYR* 4.7 5.8 - - + -
1297B LEU* 3.6 23.1 - - + -
1300B LEU* 5.7 0.9 - - + -
1301B LEU* 4.6 2.0 - - + +
1350B ILE* 3.6 35.7 - - + -
1388B MET* 3.3 34.5 + - + +
1389B PHE* 3.5 28.2 + - + +
1392B PHE* 1.3 95.0 - - + +
1394B ASN* 1.3 65.8 + - - +
1396B ALA* 3.3 7.3 + - - +
1397B ILE* 3.2 34.0 + - + +
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Residues in contact with ASN1394 (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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1389B PHE* 2.9 26.9 + - - +
1393B ILE* 1.3 75.5 - - - +
1395B PRO* 1.3 62.3 - - - +
1397B ILE* 2.9 27.7 + - - +
1398B VAL* 2.9 17.2 + - - +
1422B SER* 3.3 40.8 + - - +
1425B LEU* 4.0 11.1 - - - +
1426B GLN* 2.5 31.7 + - - +
36C ILE* 4.4 1.6 - - + +
64C TYR* 3.3 17.2 + - + +
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Residues in contact with PRO1395 (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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1390B LEU 3.2 26.9 - - - +
1391B ARG 3.9 8.3 - - - +
1392B PHE 3.8 11.4 - - - +
1393B ILE 3.6 3.1 - - - -
1394B ASN* 1.3 90.0 - - + +
1396B ALA* 1.3 59.7 + - - +
1398B VAL* 4.1 1.9 - - + +
1399B SER* 3.2 24.9 + - - +
1403B ALA* 5.2 0.2 - - - +
63C GLU* 3.8 35.1 - - + +
64C TYR* 3.6 20.4 - - + +
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Residues in contact with ALA1396 (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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1297B LEU* 3.7 30.1 - - + -
1301B LEU* 4.3 3.9 - - + +
1305B LEU* 5.5 0.7 - - - +
1392B PHE 3.9 2.6 + - - +
1393B ILE 3.3 3.9 + - - +
1394B ASN 3.2 0.8 - - - -
1395B PRO* 1.3 77.8 - - - +
1397B ILE* 1.3 66.5 + - - +
1399B SER 4.2 0.2 - - - -
1400B PRO* 3.3 26.5 - - - +
1403B ALA* 3.9 25.4 - - + -
1405B ILE* 4.2 14.0 - - + +
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Residues in contact with ILE1397 (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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1301B LEU* 4.0 20.6 - - + -
1305B LEU* 5.4 4.0 - - + +
1346B PHE* 4.4 16.6 - - + -
1350B ILE* 4.7 3.6 - - + -
1393B ILE* 3.2 24.4 + - + +
1394B ASN* 2.9 20.2 + - - +
1396B ALA* 1.3 76.9 - - - +
1398B VAL* 1.3 65.4 + - - +
1400B PRO* 3.6 3.5 - - - +
1418B LEU* 3.6 36.9 - - + +
1421B MET* 3.7 23.8 - - + -
1422B SER* 4.5 5.4 - - - -
1425B LEU* 3.8 26.7 - - + -
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Residues in contact with VAL1398 (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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1394B ASN 2.9 15.5 + - - +
1395B PRO* 4.1 5.2 - - + +
1397B ILE* 1.3 77.9 - - - +
1399B SER* 1.3 61.4 + - - +
1400B PRO* 3.3 8.3 - - - +
1415B GLU* 5.3 10.5 - - - +
1418B LEU* 4.7 11.3 - - - +
1419B LYS* 4.5 17.5 - - + -
1422B SER* 3.4 29.2 - - - +
36C ILE* 4.5 4.7 - - + -
64C TYR* 4.4 13.0 - - + -
67C MET* 3.5 36.6 - - + -
504C FMT 4.7 12.8 - - - +
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Residues in contact with SER1399 (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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1395B PRO 3.2 10.9 + - - +
1396B ALA 3.4 3.2 - - - +
1398B VAL* 1.3 86.4 + - - +
1400B PRO* 1.3 66.2 - - - +
1401B TYR 3.3 2.2 - - - -
1402B GLU* 3.3 25.4 - - - -
1403B ALA* 3.2 22.2 + - - +
66C ALA* 3.4 23.9 - - - +
67C MET* 4.4 1.7 - - - +
504C FMT 4.0 11.0 + - - -
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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