Contacts of the helix formed by residues 1403 - 1408 (chain B) in PDB entry 3GD7
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 ARG1403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1401B GLU* 3.8 7.8 + - + +
1402B ALA* 1.3 79.3 - - + +
1404B ILE* 1.3 64.3 + - - +
1405B GLU* 3.2 43.2 + - + +
1406B ALA* 3.2 24.8 + - + +
1407B MET* 3.9 3.3 - - - +
1442B PHE* 4.4 1.3 - - - -
1403D ARG* 4.6 29.7 - - - +
1405D GLU* 5.7 7.7 - - - +
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Residues in contact with ILE1404 (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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1243B LEU* 5.6 1.1 - - + -
1402B ALA 3.9 3.2 + - - -
1403B ARG* 1.3 70.4 - - - +
1405B GLU* 1.3 84.5 + - - +
1407B MET* 3.0 27.5 + - + +
1408B LEU* 3.2 13.4 + - + +
1413B PHE* 4.6 6.7 - - + -
1427B ILE* 4.2 25.1 - - + -
1430B LEU* 5.4 1.3 - - + -
1442B PHE* 3.4 41.8 - - + +
1443B ILE* 3.6 32.5 - - + -
1444B GLY 5.8 0.9 - - - +
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Residues in contact with GLU1405 (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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1403B ARG* 3.2 33.3 + - + +
1404B ILE* 1.3 92.7 - - + +
1406B ALA* 1.3 60.6 + - - +
1407B MET 3.4 0.5 + - - -
1408B LEU* 3.6 36.9 + - + +
1409B GLU* 5.2 2.8 - - - +
1445B SER* 5.8 3.5 - - - -
1403D ARG* 5.6 5.6 - - - +
1405D GLU* 5.4 4.8 - - - +
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Residues in contact with ALA1406 (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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1239B ARG* 4.8 3.3 + - - -
1373B SER* 5.1 2.9 - - - +
1381B TYR* 5.4 6.2 + - - +
1385B ARG* 5.5 2.6 + - - -
1399B LEU* 3.4 17.6 - - - +
1401B GLU* 3.7 28.0 - - + +
1403B ARG* 3.2 22.6 + - + +
1404B ILE 3.1 1.0 - - - -
1405B GLU* 1.3 79.0 - - - +
1407B MET* 1.3 57.5 + - - +
1409B GLU* 5.7 3.4 - - - +
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Residues in contact with MET1407 (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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1239B ARG* 5.7 0.4 - - - +
1241B GLY* 3.6 2.9 - - - -
1242B LEU 3.5 24.7 - - - +
1243B LEU* 4.7 4.7 - - + -
1399B LEU* 3.4 32.1 - - + +
1401B GLU* 3.5 43.3 - - + +
1403B ARG 3.9 8.1 - - - +
1404B ILE* 3.0 20.7 + - + +
1406B ALA* 1.3 79.2 - - - +
1408B LEU* 1.3 58.8 + - - +
1409B GLU* 3.1 7.2 - - - +
1410B CYS* 3.2 29.8 + - - -
1413B PHE* 3.4 28.7 - - + -
1442B PHE* 5.0 5.6 - - - -
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Residues in contact with LEU1408 (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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1404B ILE* 3.2 9.7 + - + +
1405B GLU* 3.6 43.5 + - + +
1406B ALA 3.7 0.2 - - - -
1407B MET* 1.3 75.7 - - - +
1409B GLU* 1.3 74.4 + - - +
1410B CYS 3.3 4.4 + - - +
1413B PHE* 5.1 0.3 - - - -
1427B ILE* 3.5 32.8 - - + +
1517D GLU* 4.4 13.0 - - + +
1519D LEU* 3.9 26.9 - - + -
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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