Contacts of the helix formed by residues 2173 - 2182 (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 ASP2173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2171C LEU 3.3 4.9 + - - -
2172C PRO* 1.3 70.6 - - - +
2174C SER* 1.3 59.5 + - - +
2175C LYS* 2.5 41.4 + - - +
2176C GLU* 2.6 34.4 + - + +
2177C VAL* 2.9 20.4 - - - +
2449C LYS* 5.5 2.3 + - - -
2456C ARG* 4.8 0.7 - - - +
2494C LEU* 5.1 1.0 - - - +
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Residues in contact with SER2174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172C PRO 3.3 3.3 + - - -
2173C ASP* 1.3 69.8 + - - +
2175C LYS* 1.3 65.2 + - - +
2176C GLU 3.0 2.5 + - - -
2177C VAL* 3.2 8.8 + - - +
2178C LEU* 2.6 27.4 + - - +
2449C LYS* 2.8 39.4 + - - -
2452C ILE* 4.3 24.5 - - - +
2453C ASP* 2.9 19.4 + - - -
2456C ARG* 4.6 5.4 - - - +
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Residues in contact with LYS2175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2173C ASP* 2.5 23.5 + - - +
2174C SER* 1.3 75.4 + - - +
2176C GLU* 1.3 68.7 + - + +
2178C LEU* 2.9 17.3 - - + +
2179C GLU* 2.9 49.1 + - + +
2445C GLN* 5.9 1.8 - - - +
2449C LYS* 3.9 12.3 - - - +
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Residues in contact with GLU2176 (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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2173C ASP* 2.6 37.3 + - + +
2175C LYS* 1.3 82.3 - - + +
2177C VAL* 1.3 55.9 + - - +
2179C GLU* 2.5 29.8 + - - +
2180C LYS* 2.6 49.7 + - + +
2494C LEU* 4.2 17.9 - - + +
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Residues in contact with VAL2177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172C PRO* 3.9 20.2 - - + +
2173C ASP 2.9 24.5 - - - +
2174C SER* 3.6 7.2 - - - +
2176C GLU* 1.3 71.2 - - - +
2178C LEU* 1.3 64.3 + - - +
2180C LYS* 3.9 9.3 - - - +
2181C VAL* 2.8 40.8 + - + +
2182C LEU* 3.3 8.5 + - + +
2452C ILE* 5.8 5.2 - - + -
2456C ARG* 4.7 1.8 - - - +
2491C LEU* 4.1 7.4 - - + -
2494C LEU* 4.0 6.4 - - + +
2495C TYR* 4.0 28.5 - - + +
2505C PRO* 4.6 14.1 - - + -
2509C VAL* 6.4 0.2 - - + -
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Residues in contact with LEU2178 (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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2174C SER 2.6 14.9 + - - +
2175C LYS* 2.9 20.0 - - + +
2176C GLU 2.6 2.4 + - - -
2177C VAL* 1.3 69.2 - - - +
2179C GLU* 1.3 52.6 + - + +
2182C LEU* 2.7 53.7 + - + +
2183C LEU* 2.8 39.4 + - + -
2440C VAL* 5.3 1.3 - - + -
2445C GLN* 4.1 25.6 - - + +
2448C ALA* 4.5 15.0 - - + -
2449C LYS* 4.1 35.7 - - + -
2452C ILE* 4.9 1.5 - - + +
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Residues in contact with GLU2179 (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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2175C LYS* 3.0 49.4 - - + +
2176C GLU* 2.5 20.2 + - - +
2178C LEU* 1.3 77.1 - - + +
2180C LYS* 1.3 55.8 + - + +
2181C VAL 2.4 19.3 + - - -
2182C LEU 3.4 2.1 + - - -
2183C LEU* 3.4 23.4 + - + -
2185C ARG* 3.0 23.6 + - - +
2445C GLN* 5.3 4.1 - - - +
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Residues in contact with LYS2180 (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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2176C GLU* 2.6 58.8 + - + +
2177C VAL* 3.9 6.5 - - - +
2179C GLU* 1.3 73.2 - - - +
2181C VAL* 1.3 71.6 + - + +
2185C ARG* 3.9 4.3 - - - +
2438C ARG* 3.5 9.9 + - - -
2490C GLU* 2.9 46.2 + - + +
2494C LEU* 4.2 11.2 - - + -
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Residues in contact with VAL2181 (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* 2.8 37.0 + - + +
2179C GLU 2.4 13.2 + - - -
2180C LYS* 1.3 82.3 - - + +
2182C LEU* 1.3 60.0 + - + +
2437C GLY* 4.3 0.2 - - - -
2438C ARG* 2.7 35.1 + - - +
2487C MET* 3.4 42.8 - - + -
2490C GLU* 4.2 5.4 - - + -
2491C LEU* 4.0 19.7 - - + -
2494C LEU* 5.4 0.2 - - + -
2509C VAL* 3.7 21.5 - - + +
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Residues in contact with LEU2182 (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* 3.6 11.9 - - + +
2178C LEU* 2.7 47.7 + - + +
2179C GLU 3.4 0.8 + - - -
2181C VAL* 1.3 74.7 - - + +
2183C LEU* 1.3 56.7 + - - +
2438C ARG* 2.6 3.7 - - - +
2439C ASN 2.6 32.1 + - - -
2440C VAL* 2.9 16.3 + - + +
2448C ALA* 5.1 6.5 - - + -
2452C ILE* 4.1 23.3 - - + -
2504C TYR* 5.1 5.8 - - + -
2505C PRO* 4.5 13.2 - - + +
2508C LEU* 3.9 26.5 - - + -
2509C VAL* 3.7 26.5 - - + -
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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