Contacts of the helix formed by residues 2477 - 2483 (chain B) in PDB entry 1DCX
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 SER2477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2475B TYR* 3.5 2.4 - - - +
2476B THR* 1.3 86.3 + - - +
2478B PHE* 1.3 61.0 + - - +
2479B GLU* 3.5 9.7 + - - +
2480B GLU* 2.9 39.0 + - - +
2481B LEU 3.1 8.7 + - - -
2498B ILE* 3.7 15.4 - - - +
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Residues in contact with PHE2478 (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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2477B SER* 1.3 74.2 - - - +
2479B GLU* 1.3 62.6 + - - +
2481B LEU* 3.2 6.4 + - + +
2482B THR* 3.0 28.9 + - - +
2488B ALA* 3.5 25.4 - - + +
2491B LEU* 3.4 30.7 - - + -
2492B LYS* 3.7 33.1 - - + +
2495B TYR* 3.6 17.0 - - + -
2496B SER 4.1 8.5 - - - -
2497B ASP 3.3 24.0 - - - -
2498B ILE* 3.4 30.5 - - + -
2501B MET* 3.9 28.0 - - + -
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Residues in contact with GLU2479 (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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2477B SER* 3.1 8.9 - - - +
2478B PHE* 1.3 75.6 - - - +
2480B GLU* 1.3 59.6 + - - +
2482B THR* 4.1 0.2 - - - -
2483B GLY* 2.8 31.9 + - - -
2484B GLU 3.3 17.3 + - - +
2485B LYS* 3.1 43.3 + - - +
2488B ALA* 3.6 15.0 - - + -
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Residues in contact with GLU2480 (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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2474B PRO 4.4 2.6 - - - +
2475B TYR* 3.4 27.7 - - + -
2476B THR* 2.7 44.6 + - - +
2477B SER* 2.9 21.5 + - - +
2479B GLU* 1.3 80.3 - - - +
2481B LEU* 1.3 63.1 + - - +
2483B GLY* 3.9 5.4 + - - -
2511B LYS* 4.9 5.5 - - - +
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Residues in contact with LEU2481 (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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2463B LEU* 4.3 1.8 - - + -
2475B TYR* 3.5 40.9 + - + -
2477B SER 3.1 7.4 + - - +
2478B PHE* 3.4 9.4 - - + +
2479B GLU 3.2 0.2 - - - -
2480B GLU* 1.3 82.8 - - - +
2482B THR* 1.3 63.8 + - + +
2491B LEU* 4.3 9.0 - - + -
2498B ILE* 4.4 8.7 - - + -
2501B MET* 4.2 31.9 - - + -
2506B ALA* 4.1 15.0 - - + +
2509B VAL* 4.1 18.8 - - + -
2510B GLU* 3.5 23.3 - - + +
2511B LYS* 2.9 22.9 + - - +
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Residues in contact with THR2482 (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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2478B PHE 3.0 15.1 + - - +
2481B LEU* 1.3 77.7 - - + +
2483B GLY* 1.3 63.6 + - - +
2484B GLU* 2.4 48.3 + - - +
2487B MET* 4.4 4.8 - - + +
2488B ALA 4.1 3.4 - - - +
2491B LEU* 3.8 16.2 - - + -
2509B VAL* 3.5 40.0 - - + +
2511B LYS* 3.1 18.5 - - - +
2512B PRO* 5.1 1.0 - - - +
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Residues in contact with GLY2483 (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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2479B GLU 2.8 20.0 + - - -
2480B GLU* 3.9 2.4 + - - -
2481B LEU 3.4 2.2 - - - -
2482B THR* 1.3 75.1 - - - +
2484B GLU* 1.3 59.4 + - - +
2511B LYS* 3.9 24.2 - - - +
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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