Contacts of the helix formed by residues 2502 - 2510 (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 GLU2502 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2163C MET* 5.0 10.5 - - + +
2171C LEU* 2.8 19.6 - - + +
2452C ILE* 3.1 19.8 - - - +
2455C SER* 5.4 3.1 + - - -
2456C ARG* 2.4 57.0 + - - +
2461C GLN 5.2 3.8 - - - -
2462C SER* 5.5 0.4 - - - +
2463C LEU* 3.7 1.1 - - - +
2495C TYR* 3.3 15.7 - - + +
2500C VAL 4.3 0.4 - - - +
2501C MET* 1.3 79.3 - - - +
2503C LEU* 1.3 61.7 + - - +
2505C PRO* 3.3 17.1 - - + +
2506C ALA* 3.0 28.4 + - - +
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Residues in contact with LEU2503 (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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2380C GLU* 4.8 2.0 - - + -
2383C THR* 5.9 2.5 - - + -
2384C LEU* 3.9 18.4 - - + -
2460C TYR* 4.5 19.7 - - + -
2461C GLN 4.7 4.4 + - - +
2463C LEU* 3.3 39.3 - - + +
2466C TYR* 4.0 38.6 - - + -
2467C ARG* 6.3 0.2 - - + -
2501C MET 3.7 0.2 + - - -
2502C GLU* 1.3 68.2 - - - +
2504C TYR* 1.3 71.0 + - - +
2506C ALA* 2.8 5.9 + - - +
2507C LEU* 2.8 44.5 + - + +
2521C THR* 4.0 10.1 - - + -
2525C LEU* 4.5 8.5 - - + -
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Residues in contact with TYR2504 (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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2182C LEU* 5.1 4.0 - - + -
2383C THR* 3.7 34.5 - - + -
2384C LEU* 5.3 1.3 - - - -
2386C HIS* 3.3 25.2 + - + -
2388C HIS* 2.9 33.4 + - - -
2448C ALA* 3.6 13.8 - - + +
2451C SER* 3.2 31.4 - - - +
2452C ILE* 3.7 20.4 - - + -
2455C SER* 4.5 7.5 - - - +
2503C LEU* 1.3 77.9 - - - +
2505C PRO* 1.3 75.1 - - + +
2507C LEU* 3.0 26.9 + - + +
2508C LEU* 3.3 29.4 + - + +
2522C MET* 6.3 0.4 - - + -
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Residues in contact with PRO2505 (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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2177C VAL* 4.6 12.3 - - + -
2182C LEU* 4.7 15.3 - - + -
2452C ILE* 4.5 10.5 - - + -
2455C SER* 5.9 0.4 - - - +
2495C TYR* 3.9 8.1 - - - +
2501C MET* 3.3 13.9 - - + -
2502C GLU* 3.3 38.1 - - + +
2503C LEU 3.2 4.5 - - - -
2504C TYR* 1.3 101.3 - - + +
2506C ALA* 1.3 54.0 + - - +
2507C LEU 2.6 13.3 + - - -
2508C LEU* 2.7 16.3 + - + +
2509C VAL* 3.1 15.5 + - + +
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Residues in contact with ALA2506 (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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2463C LEU* 3.1 30.3 - - + -
2481C LEU* 3.3 23.6 - - + +
2501C MET* 3.1 14.6 - - + +
2502C GLU 3.0 18.3 + - - +
2503C LEU 2.8 2.8 + - - -
2505C PRO* 1.3 75.9 - - - +
2507C LEU* 1.3 51.5 + - - +
2508C LEU 3.5 0.2 - - - -
2509C VAL* 4.6 2.5 - - - -
2510C GLU* 2.6 37.7 + - - +
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Residues in contact with LEU2507 (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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2384C LEU* 3.6 20.9 - - + -
2434C VAL* 5.1 0.7 - - - +
2435C ALA* 3.9 9.9 - - - +
2503C LEU* 2.8 47.7 + - + +
2504C TYR* 3.1 20.2 - - + +
2505C PRO 2.6 5.1 + - - -
2506C ALA* 1.3 74.7 - - - +
2508C LEU* 1.3 61.2 + - + +
2510C GLU* 3.2 20.5 - - - +
2519C GLY 5.3 0.2 + - - -
2521C THR* 3.2 28.3 - - + -
2522C MET* 3.0 50.6 - - + +
2525C LEU* 5.7 0.2 - - + -
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Residues in contact with LEU2508 (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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2182C LEU* 3.9 19.3 - - + -
2386C HIS 4.1 7.2 - - - +
2387C TRP* 5.6 0.9 - - + -
2389C PRO* 3.3 17.0 - - + -
2434C VAL* 2.9 46.2 - - + +
2435C ALA 2.7 19.8 - - - +
2437C GLY* 3.3 10.9 + - - -
2438C ARG 6.2 0.2 - - - +
2440C VAL* 3.8 26.5 - - + -
2448C ALA* 5.4 0.4 - - + -
2504C TYR* 3.3 40.8 - - + +
2505C PRO 2.7 10.1 + - - +
2507C LEU* 1.3 78.8 - - + +
2509C VAL* 1.3 55.9 + - - +
2522C MET* 6.3 1.6 - - + -
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Residues in contact with VAL2509 (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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2181C VAL* 3.7 33.2 - - + +
2182C LEU* 3.7 17.9 - - + -
2435C ALA 3.2 3.5 - - - +
2436C GLY 3.6 4.7 - - - +
2437C GLY* 4.0 4.9 - - - -
2481C LEU* 4.7 3.4 - - + -
2482C THR* 3.2 32.3 - - + +
2487C MET* 4.2 12.1 - - - -
2491C LEU* 3.9 23.1 - - + -
2501C MET* 5.9 0.2 - - + -
2505C PRO* 3.1 14.2 + - + +
2506C ALA* 4.3 4.5 - - - +
2508C LEU* 1.3 75.3 - - - +
2510C GLU* 1.3 73.0 + - - +
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Residues in contact with GLU2510 (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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2435C ALA* 2.3 21.2 - - + +
2436C GLY 3.9 0.7 - - - +
2463C LEU* 6.2 0.4 - - + -
2475C TYR* 3.3 17.5 + - + +
2481C LEU* 3.2 26.9 - - + +
2506C ALA 2.6 21.0 + - - +
2507C LEU* 3.2 14.4 - - - +
2508C LEU 3.4 0.8 - - - -
2509C VAL* 1.3 85.0 - - - +
2511C LYS* 1.3 55.1 + - - +
2512C PRO* 2.7 11.1 - - - +
2519C GLY* 2.9 32.2 + - - -
2520C GLU 2.9 6.2 + - - -
2521C THR* 2.7 41.1 + - - +
2522C MET* 3.6 9.0 + - - +
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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