Contacts of the helix formed by residues 1494 - 1501 (chain A) in PDB entry 5DKD
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 LEU1494 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489A PRO* 3.8 37.0 - - + +
1490A SER 3.0 6.2 + - - +
1491A ARG 3.6 2.2 - - - -
1493A GLU* 1.3 81.6 - - - +
1495A PRO* 1.3 67.2 - - + +
1496A GLU* 3.2 10.1 - - + +
1497A TYR* 3.1 35.9 + - + +
1498A TYR* 3.3 13.2 - - - -
1539A PHE* 3.9 27.6 - - + -
1605A 5BW 3.8 29.2 - - + +
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Residues in contact with PRO1495 (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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1491A ARG* 3.2 18.6 - - + +
1492A LYS* 3.8 7.6 - - - +
1493A GLU 3.7 4.9 - - - +
1494A LEU* 1.3 91.1 - - + +
1496A GLU* 1.3 63.4 + - - +
1498A TYR* 3.1 17.6 + - + +
1499A GLU* 3.1 25.4 + - - +
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Residues in contact with GLU1496 (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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1494A LEU* 3.2 9.4 - - + +
1495A PRO* 1.3 79.8 - - + +
1497A TYR* 1.3 61.8 + - - +
1499A GLU* 3.2 12.9 + - + +
1500A LEU* 3.0 27.0 + - + +
1539A PHE* 3.3 30.7 - - + -
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Residues in contact with TYR1497 (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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1488A LEU* 3.4 39.0 - - + +
1494A LEU* 3.1 29.6 + - + +
1496A GLU* 1.3 77.0 - - - +
1498A TYR* 1.3 68.9 + + + +
1501A ILE* 2.9 58.8 + - + +
1504A PRO* 4.0 8.7 - - + -
1505A VAL 4.8 0.7 + - - -
1535A ASN* 3.5 18.2 + - - +
1539A PHE* 3.5 41.5 - + + -
1605A 5BW 2.8 47.5 + - - -
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Residues in contact with TYR1498 (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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1488A LEU* 3.8 14.0 - - + +
1489A PRO 2.7 26.4 + - - -
1490A SER* 3.8 1.6 - - - -
1491A ARG* 3.5 76.4 + - + +
1494A LEU* 3.3 19.1 - - + -
1495A PRO* 3.1 7.7 + - + +
1497A TYR* 1.3 85.7 - + + +
1499A GLU* 1.3 64.4 + - - +
1501A ILE 3.6 13.8 - - - +
1504A PRO* 3.9 28.0 - - + +
1603A EDO 5.7 5.6 - - - -
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Residues in contact with GLU1499 (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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1495A PRO* 3.1 28.1 + - - +
1496A GLU* 3.2 10.5 + - + +
1498A TYR* 1.3 79.2 - - - +
1500A LEU* 1.3 61.5 + - - +
1501A ILE 4.9 0.7 - - - +
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Residues in contact with LEU1500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1496A GLU* 3.0 18.9 + - + +
1497A TYR 4.1 1.8 - - - +
1499A GLU* 1.3 80.3 - - - +
1501A ILE* 1.3 68.4 + - + +
1502A ARG* 3.7 7.8 + - - +
1538A THR* 3.8 37.0 - - + +
1539A PHE* 3.9 22.9 - - + +
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Residues in contact with ILE1501 (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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1497A TYR* 2.9 51.8 + - + +
1498A TYR 3.6 14.3 - - - +
1499A GLU 5.0 0.7 - - - -
1500A LEU* 1.3 88.2 - - + +
1502A ARG* 1.3 63.5 + - - +
1503A LYS 4.0 0.4 - - - +
1504A PRO* 3.8 20.5 - - + +
1535A ASN* 3.6 45.3 - - - +
1538A THR* 3.6 37.2 - - + -
1539A PHE* 4.3 4.0 - - + +
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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