Contacts of the helix formed by residues 1397 - 1404 (chain C) in PDB entry 6PUO
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 MET1397 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1394C PRO* 3.7 26.2 - - + +
1395C GLY 3.5 0.4 - - - -
1396C GLU* 1.3 76.6 - - - +
1398C LEU* 1.3 52.7 + - - +
1399C PRO 3.3 1.1 - - - -
1400C ARG* 3.0 16.2 + - + +
1401C LYS* 2.4 35.5 + - - +
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Residues in contact with LEU1398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348C LEU* 4.2 14.0 - - + +
1390C GLY* 4.7 4.3 + - - +
1391C SER 4.2 2.4 - - - +
1392C ARG* 3.7 24.5 - - + -
1394C PRO* 3.3 26.1 + - - +
1395C GLY 3.6 6.7 - - - +
1397C MET* 1.3 74.4 - - - +
1399C PRO* 1.4 66.3 - - + +
1401C LYS* 3.7 10.1 - - - +
1402C LEU* 2.9 26.9 + - - +
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Residues in contact with PRO1399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348C LEU* 3.9 19.3 - - + -
1350C PRO* 5.9 9.0 - - + -
1395C GLY 4.2 2.7 - - - +
1396C GLU* 3.3 20.9 - - - +
1398C LEU* 1.4 89.8 - - + +
1400C ARG* 1.3 51.0 + - - +
1402C LEU* 3.2 6.9 + - + +
1403C LYS* 2.6 39.2 + - - +
1412C PRO 5.7 2.7 - - - +
1415C GLU 6.2 0.2 - - - -
1416C ASN* 5.4 11.2 - - + +
1419C LYS* 4.8 17.7 - - + -
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Residues in contact with ARG1400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396C GLU 4.6 0.4 + - - +
1397C MET* 3.0 23.3 + - + +
1399C PRO* 1.3 76.4 - - - +
1401C LYS* 1.3 60.4 + - - +
1403C LYS* 4.0 3.6 - - - +
1404C ARG* 2.5 41.6 + - + +
1408C GLN 5.8 0.7 - - - +
1412C PRO* 5.0 18.4 - - + +
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Residues in contact with LYS1401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390C GLY* 5.0 4.1 - - - -
1391C SER 4.0 14.8 - - - +
1393C GLU* 6.1 0.4 - - + -
1394C PRO* 4.3 11.0 - - + -
1397C MET 2.4 30.4 + - - +
1398C LEU* 3.8 11.7 - - - +
1399C PRO 3.3 0.2 - - - -
1400C ARG* 1.3 69.4 - - - +
1402C LEU* 1.3 61.0 + - - +
1404C ARG* 4.7 3.3 + - - +
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Residues in contact with LEU1402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350C PRO* 5.6 1.8 - - + -
1388C PRO* 3.6 23.8 - - - +
1389C GLY* 3.7 2.9 - - - -
1390C GLY* 3.4 30.7 - - - +
1398C LEU 2.9 16.0 + - - +
1399C PRO* 3.4 7.2 - - + +
1401C LYS* 1.3 80.4 - - - +
1403C LYS* 1.3 58.8 + - + +
1404C ARG 3.7 1.2 + - - -
1405C ILE* 4.8 4.9 + - - +
1406C LEU* 4.7 4.2 + - - +
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Residues in contact with LYS1403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388C PRO* 5.8 4.5 - - + +
1399C PRO 2.6 19.5 + - - +
1400C ARG* 3.3 5.3 - - - -
1402C LEU* 1.3 76.4 - - + +
1404C ARG* 1.3 59.9 + - - +
1405C ILE 3.3 0.9 - - - -
1406C LEU* 3.4 15.7 - - + +
1407C ARG* 2.8 43.9 + - + +
1408C GLN 3.8 6.4 - - - +
1412C PRO* 5.5 0.6 - - + +
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Residues in contact with ARG1404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400C ARG* 2.5 25.0 + - + +
1401C LYS* 4.6 3.6 - - - +
1402C LEU 3.7 1.6 - - - -
1403C LYS* 1.3 74.7 - - - +
1405C ILE* 1.3 61.9 + - - +
1406C LEU 3.5 0.3 + - - -
1407C ARG 4.7 0.7 + - - -
1408C GLN* 4.5 13.4 + - - +
1468C ASP* 4.1 8.7 - - - +
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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