Contacts of the helix formed by residues 2105 - 2122 (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 ILE2105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2102B ILE* 3.3 33.7 - - - +
2103B VAL 2.8 4.1 + - - -
2105B ASN* 1.3 81.4 - - - +
2106B PRO* 1.3 55.1 - - - +
2107B PHE* 3.1 10.1 + - - +
2108B LEU* 2.5 73.0 + - + +
2109B ARG* 2.8 11.1 + - - -
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Residues in contact with PRO2106 (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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2104B ASN 5.3 1.1 - - - +
2105B ILE* 1.3 97.6 - - - +
2107B PHE* 1.3 64.5 + - - +
2109B ARG* 3.6 9.6 - - + +
2110B SER* 2.8 30.5 + - - -
2360B LYS* 5.0 3.7 + - - +
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Residues in contact with PHE2107 (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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2105B ILE* 2.9 9.3 + - - +
2106B PRO* 1.3 79.9 - - - +
2108B LEU* 1.3 65.4 + - + +
2110B SER* 3.6 6.7 - - - -
2111B LEU* 2.9 53.1 + - + +
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Residues in contact with LEU2108 (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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2102B ILE* 5.0 4.3 - - + -
2103B VAL* 4.1 26.5 - - + -
2105B ILE* 2.5 52.2 + - + +
2107B PHE* 1.3 76.8 - - + +
2109B ARG* 1.3 54.8 + - - +
2111B LEU* 3.0 21.2 + - + +
2112B ILE* 2.7 49.9 + - + +
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Residues in contact with ARG2109 (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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2103B VAL* 3.8 12.5 + - - +
2104B ASN* 4.0 19.9 + - - +
2105B ILE 2.8 13.9 + - - +
2106B PRO* 3.6 13.2 - - + +
2108B LEU* 1.3 73.1 - - - +
2110B SER* 1.3 56.0 + - - +
2112B ILE 3.3 0.7 + - - -
2113B MET* 2.9 27.8 + - - +
2346B GLU* 4.1 11.7 + - - -
2357B PHE* 3.3 33.3 - - + -
2358B LYS* 2.9 34.4 + - - +
2359B LEU 2.9 26.7 + - - -
2360B LYS* 3.4 36.2 - - + +
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Residues in contact with SER2110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2106B PRO 2.8 16.6 + - - -
2107B PHE* 3.6 8.1 - - - -
2109B ARG* 1.3 72.0 - - - +
2111B LEU* 1.3 69.0 + - - +
2113B MET* 3.2 6.0 + - - +
2114B LYS* 2.8 24.7 + - - +
2360B LYS* 3.0 29.6 + - - +
2362B ASP* 4.4 0.9 + - - -
2365B LEU* 3.9 23.0 - - - +
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Residues in contact with LEU2111 (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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2107B PHE* 2.9 45.1 + - + +
2108B LEU* 3.1 22.4 - - + +
2110B SER* 1.3 79.1 - - - +
2112B ILE* 1.3 73.4 + - + +
2114B LYS* 3.3 10.2 + - - +
2115B TYR* 3.3 18.5 + - + +
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Residues in contact with ILE2112 (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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2093B LEU* 5.2 3.4 - - + -
2100B TRP* 4.2 20.9 - - + -
2103B VAL* 3.9 22.4 - - + -
2108B LEU* 2.7 31.1 + - + +
2111B LEU* 1.3 80.9 - - + +
2113B MET* 1.3 66.9 + - - +
2115B TYR* 2.9 21.1 + - + +
2116B VAL* 2.8 21.5 + - + +
2357B PHE* 3.5 32.3 - - + -
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Residues in contact with MET2113 (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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2109B ARG 2.9 20.5 + - - +
2110B SER* 3.7 4.3 - - - +
2112B ILE* 1.3 74.1 - - - +
2114B LYS* 1.3 61.0 + - - +
2116B VAL* 3.5 16.8 + - + +
2117B LEU* 3.0 54.0 + - + +
2345B ILE* 4.6 11.0 - - + -
2357B PHE* 3.5 6.2 - - + -
2359B LEU* 3.8 24.2 - - + -
2360B LYS* 3.2 51.4 - - + +
2365B LEU* 3.6 17.7 - - + -
2535B MET* 6.4 0.4 - - - -
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Residues in contact with LYS2114 (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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2110B SER 2.8 11.5 + - - +
2111B LEU* 3.3 15.3 - - - +
2112B ILE 3.0 0.2 - - - -
2113B MET* 1.3 78.4 - - - +
2115B TYR* 1.3 56.0 + - - +
2117B LEU* 3.1 8.5 + - + +
2118B THR* 2.8 41.7 + - + +
2365B LEU* 3.1 43.7 - - + +
2366B LEU* 6.1 0.2 - - + -
2368B ASN* 3.1 29.1 + - - +
2369B GLN* 3.1 20.6 + - - +
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Residues in contact with TYR2115 (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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2084B PRO* 4.9 6.6 - - - +
2089B VAL* 3.9 34.7 - - + +
2093B LEU* 5.8 3.8 - - + -
2111B LEU* 3.3 10.2 + - + +
2112B ILE* 2.9 19.6 + - + +
2114B LYS* 1.3 78.6 - - - +
2116B VAL* 1.3 59.3 + - + +
2118B THR* 3.3 8.0 + - - -
2119B SER* 2.6 64.5 + - - -
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Residues in contact with VAL2116 (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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2701 ACD 5.7 3.4 - - - +
2093B LEU* 6.1 7.0 - - + -
2112B ILE* 2.8 22.9 - - + +
2113B MET* 3.5 34.5 - - + +
2115B TYR* 1.3 85.7 - - + +
2117B LEU* 1.3 65.3 + - + +
2119B SER* 2.8 17.3 + - - -
2120B ARG* 3.7 27.2 + - - +
2355B TYR* 6.2 3.4 - - + -
2357B PHE* 4.3 13.2 - - + -
2359B LEU* 4.5 10.1 - - + -
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Residues in contact with LEU2117 (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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2113B MET* 3.0 57.1 + - + +
2114B LYS* 3.4 5.2 - - - +
2115B TYR 3.1 0.2 - - - -
2116B VAL* 1.3 80.3 - - + +
2118B THR* 1.3 63.8 + - - +
2120B ARG 3.2 10.6 + - - -
2121B SER* 3.3 13.2 + - - -
2345B ILE* 6.4 0.4 - - + -
2360B LYS 5.1 1.8 - - - +
2362B ASP 5.1 2.5 - - - +
2365B LEU* 4.0 23.8 - - + -
2366B LEU* 4.3 24.9 - - + -
2531B LEU* 3.4 35.0 - - + +
2535B MET* 4.7 12.1 - - + -
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Residues in contact with THR2118 (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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2114B LYS* 2.8 31.9 + - + +
2115B TYR* 3.3 9.7 + - - -
2117B LEU* 1.3 75.6 - - + +
2119B SER* 1.3 64.4 + - - +
2120B ARG 3.1 0.9 + - - -
2121B SER* 3.3 25.1 - - - +
2122B TYR* 4.4 4.0 + - - -
2366B LEU* 4.7 5.4 - - + -
2369B GLN* 3.4 40.8 - - + +
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Residues in contact with SER2119 (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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2115B TYR* 2.6 54.9 + - - -
2116B VAL* 2.8 22.5 + - - -
2118B THR* 1.3 74.0 + - - +
2120B ARG* 1.3 70.2 + - - +
2122B TYR* 3.6 22.2 - - - -
2123B LEU* 4.2 1.6 - - - +
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Residues in contact with ARG2120 (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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2701 ACD 3.0 31.8 + - - -
2116B VAL* 3.7 24.4 + - - +
2117B LEU 3.2 2.8 + - - +
2118B THR 3.1 0.4 - - - -
2119B SER* 1.3 88.5 + - - +
2121B SER* 1.3 68.0 + - - +
2122B TYR 3.1 0.3 + - - -
2123B LEU* 3.0 32.7 + - - +
2355B TYR* 4.6 5.5 + - - -
2523B VAL* 4.4 2.0 - - - +
2524B GLU* 3.1 34.9 + - - -
2527B ALA* 3.7 23.1 - - + +
2528B PRO* 4.3 21.8 - - + +
2531B LEU* 3.5 22.9 - - + -
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Residues in contact with SER2121 (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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2117B LEU 3.3 14.0 + - - -
2118B THR* 3.3 22.5 - - - +
2120B ARG* 1.3 76.0 - - - +
2122B TYR* 1.3 53.5 + - - -
2123B LEU 2.5 15.1 + - - -
2124B ILE* 3.6 13.2 + - - +
2366B LEU* 5.2 3.1 - - - +
2369B GLN* 5.8 0.9 - - - +
2370B GLN 5.3 6.6 + - - -
2371B PHE* 4.6 15.5 - - - -
2531B LEU* 4.0 9.7 - - - +
2532B LYS* 6.0 2.3 - - - +
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Residues in contact with TYR2122 (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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2044B ARG* 3.7 14.3 + - - -
2083B LYS* 3.7 16.9 + - + +
2118B THR 4.4 2.7 + - - +
2119B SER* 3.6 23.8 - - - -
2120B ARG 3.1 2.6 + - - -
2121B SER* 1.3 73.9 - - - +
2123B LEU* 1.3 84.3 + - + +
2124B ILE 5.1 1.9 - - - +
2471B SER* 3.1 24.7 + - - -
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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