Contacts of the helix formed by residues 1605 - 1614 (chain A) in PDB entry 6J8H
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 SER1605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1599A ILE* 4.2 16.1 - - - +
1603A PHE 5.6 0.2 - - - -
1604A VAL* 1.3 85.8 - - - +
1606A PRO* 1.3 75.8 - - - +
1607A THR* 3.7 4.7 + - - -
1608A LEU* 4.1 22.2 + - - +
1609A PHE* 4.2 1.9 + - - +
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Residues in contact with PRO1606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605A SER* 1.3 88.7 - - - +
1607A THR* 1.3 72.2 + - - +
1609A PHE* 3.0 30.1 + - + +
1610A ARG* 3.3 14.3 + - - +
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Residues in contact with THR1607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A TYR* 3.5 8.7 - - + +
1605A SER* 3.4 5.8 - - - -
1606A PRO* 1.3 82.1 - - - +
1608A LEU* 1.3 66.4 + - - +
1609A PHE 3.1 1.5 + - - -
1610A ARG* 3.2 39.8 + - - +
1611A VAL* 3.2 21.4 + - + +
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Residues in contact with LEU1608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1599A ILE* 3.9 23.1 - - + -
1605A SER* 4.1 20.0 + - - +
1606A PRO 3.4 0.8 - - - -
1607A THR* 1.3 80.2 - - - +
1609A PHE* 1.3 56.8 + - - +
1611A VAL* 3.4 9.6 + - + +
1612A ILE* 2.9 48.6 + - + +
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Residues in contact with PHE1609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLN* 5.9 0.2 - - - -
1596A ALA* 2.8 51.4 - - + -
1599A ILE* 4.4 15.4 - - + +
1600A GLU* 3.7 22.0 - - + -
1605A SER 4.2 5.7 + - - +
1606A PRO* 3.0 18.7 + - + +
1608A LEU* 1.3 77.4 - - - +
1610A ARG* 1.3 73.4 + - + +
1612A ILE* 3.1 8.7 + - - +
1613A ARG* 3.1 54.6 + - + +
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Residues in contact with ARG1610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLN* 3.9 32.5 - - + +
266A LEU* 2.3 40.9 + - + +
270A ASN* 4.8 11.1 + - - +
378A TYR* 2.1 38.4 + - - -
1606A PRO* 3.3 13.2 + - - +
1607A THR* 3.2 33.8 + - - +
1609A PHE* 1.3 83.5 - - + +
1611A VAL* 1.3 64.2 + - - +
1613A ARG* 3.2 13.6 + - - +
1614A LEU* 3.4 17.6 + - - +
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Residues in contact with VAL1611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 4.6 12.8 - - + -
378A TYR* 5.1 4.0 - - + +
1607A THR* 3.2 24.2 - - + +
1608A LEU* 3.8 12.8 - - + +
1609A PHE 3.2 0.6 - - - -
1610A ARG* 1.3 78.5 - - + +
1612A ILE* 1.3 63.7 + - + +
1614A LEU* 3.1 36.6 - - + +
1615A ALA 4.4 0.3 + - - -
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Residues in contact with ILE1612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1592A GLY* 3.6 31.8 - - - +
1595A LEU* 4.3 23.8 - - + -
1596A ALA* 4.4 8.3 - - + +
1599A ILE* 4.2 12.3 - - + -
1608A LEU* 2.9 39.9 + - + +
1609A PHE* 3.1 10.3 + - - +
1611A VAL* 1.3 79.7 - - + +
1613A ARG* 1.3 62.1 + - - +
1614A LEU 3.2 1.0 + - - -
1615A ALA* 3.3 19.8 + - - +
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Residues in contact with ARG1613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLN* 3.1 44.1 + - - +
268A MET* 5.9 2.8 - - - +
1535A GLU* 3.0 26.9 + - - -
1551A ASN* 5.1 3.8 + - - -
1592A GLY* 5.5 3.6 - - - +
1596A ALA* 4.9 6.3 - - + -
1609A PHE* 3.1 50.1 + - + +
1610A ARG 3.2 4.7 + - - +
1612A ILE* 1.3 72.2 - - - +
1614A LEU* 1.3 52.6 + - - +
1615A ALA* 2.6 13.8 + - - -
1616A ARG* 2.6 60.5 + - - +
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Residues in contact with LEU1614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE* 4.3 24.7 - - + +
265A GLN* 3.4 35.4 - - + -
266A LEU* 3.9 26.7 - - + -
1610A ARG 3.4 8.0 + - - +
1611A VAL* 3.1 25.7 + - + +
1612A ILE 3.1 0.8 - - - -
1613A ARG* 1.3 77.4 - - - +
1615A ALA* 1.3 60.8 + - - +
1616A ARG 3.2 0.4 - - - -
1617A ILE* 3.2 32.4 + - + +
1618A GLY 4.2 0.7 + - - -
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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