Contacts of the helix formed by residues 2387 - 2391 (chain C) in PDB entry 1DDX
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 TRP2387 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2198C PHE* 3.7 18.4 - + - -
2202C ALA* 4.4 5.8 - - + -
2348C TYR* 3.5 18.4 - - - -
2352C LEU* 3.4 15.9 - - + -
2384C LEU 2.7 29.9 + - - -
2385C TYR* 2.3 29.7 + + + +
2386C HIS* 1.3 68.2 - - - +
2388C HIS* 1.3 65.1 + - - +
2389C PRO* 3.3 6.7 - - - -
2390C LEU* 3.1 45.3 + - + +
2434C VAL* 4.5 9.4 - - + -
2508C LEU* 5.6 0.7 - - + -
2518C PHE* 3.0 33.6 - + - -
2522C MET* 2.9 17.4 - - + -
2701C PGX 2.9 49.8 - - + -
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Residues in contact with HIS2388 (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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2385C TYR* 5.8 3.9 + + - -
2386C HIS* 3.3 26.8 + - + +
2387C TRP* 1.3 71.3 - - - +
2389C PRO* 1.3 59.8 - - + +
2390C LEU 2.6 0.5 + - - -
2391C LEU* 2.6 45.7 + - + +
2440C VAL* 4.0 5.8 - - + +
2441C PRO* 3.8 4.0 - - - +
2444C VAL* 3.5 29.2 - - + -
2447C VAL* 2.9 35.9 - - + +
2448C ALA* 3.7 12.7 - - - +
2451C SER* 3.5 6.3 - - - -
2504C TYR* 2.9 28.9 + - - -
2508C LEU* 4.7 0.6 - - - +
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Residues in contact with PRO2389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2184C ARG* 2.7 19.2 + - - +
2387C TRP 3.4 0.4 - - - -
2388C HIS* 1.3 93.9 - - + +
2390C LEU* 1.3 57.9 + - - +
2432C GLY* 3.0 15.4 - - - -
2433C ARG 2.8 23.0 - - - +
2434C VAL* 3.2 35.0 - - + +
2439C ASN* 3.2 25.3 + - + +
2440C VAL* 4.0 12.8 - - + -
2441C PRO* 4.2 0.2 - - - -
2508C LEU* 3.3 19.1 - - + -
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Residues in contact with LEU2390 (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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2194C SER* 4.9 2.2 - - - -
2196C MET* 3.7 2.5 - - - +
2198C PHE* 3.7 32.5 - - + -
2199C ALA* 4.2 18.2 - - + +
2202C ALA* 5.1 0.9 - - + -
2387C TRP* 3.1 38.5 + - + +
2388C HIS 2.6 4.8 + - - -
2389C PRO* 1.3 74.3 - - - +
2391C LEU* 1.3 60.9 + - - +
2392C PRO* 3.3 1.1 - - - -
2431C ALA* 3.1 24.7 - - + +
2432C GLY 2.8 35.5 + - - +
2434C VAL* 3.3 15.7 - - + -
2517C ILE* 3.4 18.2 - - + -
2518C PHE* 5.8 0.4 - - + -
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Residues in contact with LEU2391 (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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2184C ARG* 2.5 31.7 + - - -
2187C PHE* 4.4 0.3 - - - -
2196C MET* 5.1 0.2 - - - -
2199C ALA* 6.0 1.3 - - - -
2200C PHE* 5.9 2.9 - - + -
2388C HIS* 2.6 24.4 + - + +
2389C PRO 3.4 0.2 - - - +
2390C LEU* 1.3 73.1 - - - +
2392C PRO* 1.3 69.8 - - + +
2395C PHE* 3.2 36.8 - - + -
2404C PHE* 3.3 18.8 - - + -
2441C PRO* 3.7 7.4 - - + -
2444C VAL* 3.3 33.2 - - + -
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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
------------------------------------------------------------
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