Contacts of the helix formed by residues 2079 - 2099 (chain B) in PDB entry 4DJ9
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 VAL2079 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 4.9 14.4 - - + +
2078B VAL* 1.3 70.2 - - + +
2080B LEU* 1.3 61.1 + - + +
2082B ASN* 3.4 10.4 + - + +
2083B ALA* 3.0 28.6 + - - +
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Residues in contact with LEU2080 (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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54A LEU* 4.0 21.5 - - + -
57A VAL* 3.9 15.3 - - + -
58A GLY* 3.9 24.0 - - - +
61A THR* 3.4 37.7 - - + +
74A MET* 3.8 13.2 - - + -
78A PHE* 5.3 0.9 - - + -
126A PHE* 3.8 27.1 - - + -
2078B VAL* 3.5 6.7 - - + +
2079B VAL* 1.3 76.5 - - + +
2081B ILE* 1.3 61.2 + - + +
2083B ALA* 3.3 5.7 + - + +
2084B VAL* 3.0 33.0 + - - +
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Residues in contact with ILE2081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 4.0 18.4 - - + -
12A ILE* 3.8 23.4 - - + +
123A LEU* 4.2 9.0 - - + -
126A PHE* 3.9 29.8 - - + -
130A GLU* 6.5 1.1 - - + -
2078B VAL* 3.4 40.1 + - + +
2079B VAL 3.4 0.2 - - - -
2080B LEU* 1.3 74.7 - - + +
2082B ASN* 1.3 62.2 + - - +
2084B VAL* 3.2 10.2 + - - +
2085B LYS* 3.0 25.9 + - - +
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Residues in contact with ASN2082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078B VAL 3.0 30.1 + - - +
2079B VAL* 3.7 11.8 + - + +
2080B LEU 3.3 0.2 - - - -
2081B ILE* 1.3 79.7 - - - +
2083B ALA* 1.3 57.7 + - - +
2085B LYS* 3.3 31.9 + - + +
2086B ASP* 3.0 35.3 + - - +
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Residues in contact with ALA2083 (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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50A ALA 4.7 1.2 - - - +
53A ASN* 5.0 6.1 - - + +
54A LEU* 4.1 30.2 - - + +
57A VAL* 5.2 7.2 - - + -
2079B VAL 3.0 17.7 + - - +
2080B LEU* 3.3 8.7 + - + +
2082B ASN* 1.3 74.6 - - - +
2084B VAL* 1.4 61.5 + - - +
2086B ASP* 3.5 11.5 + - - +
2087B VAL* 3.3 26.2 + - - +
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Residues in contact with VAL2084 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.2 6.1 - - + -
13A LEU* 5.0 0.2 - - + -
54A LEU* 3.8 26.5 - - + -
119A THR* 3.8 23.4 - - - +
122A LEU* 4.4 8.3 - - + -
123A LEU* 3.7 42.0 - - + -
126A PHE* 4.2 11.7 - - + -
2080B LEU 3.0 18.8 + - - +
2081B ILE 3.2 7.8 + - - +
2083B ALA* 1.4 73.9 - - - +
2085B LYS* 1.3 58.1 + - - +
2087B VAL* 3.2 5.2 + - - +
2088B ALA* 3.0 25.5 + - - +
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Residues in contact with LYS2085 (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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11A SER* 5.9 0.9 - - - -
12A ILE* 4.0 37.4 - - + +
2081B ILE* 3.0 12.4 + - - +
2082B ASN* 3.3 31.0 - - - +
2084B VAL* 1.3 73.4 - - - +
2086B ASP* 1.4 62.3 + - - +
2088B ALA* 3.4 3.0 + - + +
2089B LYS* 3.0 39.5 + - + +
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Residues in contact with ASP2086 (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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50A ALA* 3.8 15.0 - - + +
53A ASN* 5.3 7.3 + - - +
2082B ASN* 3.0 20.7 + - - +
2083B ALA* 3.6 12.7 - - - +
2084B VAL 3.3 0.4 - - - -
2085B LYS* 1.4 78.8 - - - +
2087B VAL* 1.4 57.6 + - - +
2089B LYS* 3.5 7.0 + - - +
2090B ALA* 3.1 29.3 + - - +
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Residues in contact with VAL2087 (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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47A VAL* 5.3 3.2 - - + +
50A ALA* 3.5 36.6 - - + +
51A VAL* 3.8 16.4 - - + +
54A LEU* 3.8 17.0 - - + -
81A VAL* 4.6 1.8 - - + -
115A ILE* 3.6 29.8 - - + -
119A THR* 3.8 13.5 - - + -
2083B ALA 3.4 13.9 - - - +
2084B VAL 3.2 8.6 + - - +
2086B ASP* 1.4 75.6 - - - +
2088B ALA* 1.3 56.2 + - - +
2090B ALA* 3.3 3.8 + - - +
2091B LEU* 3.0 27.5 + - - +
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Residues in contact with ALA2088 (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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12A ILE* 3.6 33.0 - - + +
13A LEU* 4.4 7.2 - - + -
16A VAL* 4.1 19.8 - - + +
115A ILE* 6.0 0.4 - - - -
119A THR* 5.4 2.7 - - + +
2084B VAL 3.0 12.0 + - - +
2085B LYS 3.7 7.0 - - - +
2087B VAL* 1.3 75.2 - - - +
2089B LYS* 1.3 56.7 + - - +
2091B LEU* 3.4 8.9 + - - +
2092B GLY* 3.0 25.5 + - - -
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Residues in contact with LYS2089 (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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2085B LYS* 3.0 26.1 + - + +
2086B ASP* 3.7 7.6 - - - +
2088B ALA* 1.3 71.6 - - - +
2090B ALA* 1.3 60.4 + - - +
2092B GLY* 3.4 2.4 + - - -
2093B ASP* 3.1 43.7 + - - +
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Residues in contact with ALA2090 (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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43A PRO 4.6 1.9 - - - +
46A ALA* 3.8 30.4 - - + +
47A VAL* 3.5 22.2 - - + +
50A ALA* 4.4 3.6 - - + -
2086B ASP 3.1 16.7 + - - +
2087B VAL 3.3 4.7 + - - +
2089B LYS* 1.3 74.7 - - - +
2091B LEU* 1.4 57.2 + - - +
2093B ASP* 3.3 12.7 + - - +
2094B LEU* 3.0 22.0 + - - +
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Residues in contact with LEU2091 (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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16A VAL* 3.8 17.7 - - + -
20A ILE* 4.2 5.2 - - + -
47A VAL* 3.9 8.0 - - + +
88A LEU* 3.7 29.8 - - + -
112A SER* 3.8 33.4 - - - +
115A ILE* 3.7 28.5 - - + -
116A LEU* 4.4 4.0 - - + +
2087B VAL 3.0 17.2 + - - +
2088B ALA* 3.7 7.0 - - - +
2089B LYS 3.3 0.2 - - - -
2090B ALA* 1.4 75.3 - - - +
2092B GLY* 1.3 58.9 + - - +
2094B LEU* 3.1 10.9 + - + +
2095B ILE* 3.0 38.2 + - + +
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Residues in contact with GLY2092 (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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16A VAL* 4.1 4.9 - - - +
19A GLN* 3.3 30.5 + - - +
2088B ALA 3.0 14.5 + - - -
2089B LYS 3.8 3.8 - - - -
2090B ALA 3.4 0.2 - - - -
2091B LEU* 1.3 75.9 - - - +
2093B ASP* 1.4 61.6 + - - +
2095B ILE* 3.4 0.6 + - - -
2096B SER* 3.1 22.6 + - - -
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Residues in contact with ASP2093 (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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43A PRO* 4.5 9.0 - - + +
46A ALA* 6.0 3.4 - - + +
2089B LYS* 3.1 29.5 + - - +
2090B ALA* 3.4 11.9 - - - +
2091B LEU 3.3 0.2 - - - -
2092B GLY* 1.4 74.7 - - - +
2094B LEU* 1.4 61.9 + - - +
2096B SER* 3.0 20.2 + - - -
2097B ALA* 3.1 13.9 + - - +
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Residues in contact with LEU2094 (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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40A LEU* 3.9 15.7 - - + -
43A PRO* 3.7 27.1 - - + +
44A VAL* 3.5 35.0 - - + +
47A VAL* 4.1 12.3 - - + -
88A LEU* 4.0 35.7 - - + -
108A LEU* 4.4 12.1 - - + -
112A SER* 5.7 0.2 - - - +
2090B ALA 3.0 13.4 + - - +
2091B LEU* 3.1 11.9 + - + +
2093B ASP* 1.4 76.1 - - - +
2095B ILE* 1.3 63.5 + - + +
2097B ALA* 3.0 14.7 + - - +
2098B THR* 3.2 15.5 + - - +
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Residues in contact with ILE2095 (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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16A VAL* 4.2 8.1 - - + -
19A GLN* 3.8 28.7 - - + +
20A ILE* 3.7 29.6 - - + -
23A LEU* 4.0 30.1 - - + -
108A LEU* 6.3 1.3 - - + -
112A SER* 3.8 20.4 - - - +
2091B LEU* 3.0 32.7 + - + +
2092B GLY 4.0 3.6 - - - +
2094B LEU* 1.3 76.9 - - + +
2096B SER* 1.3 60.7 + - - +
2098B THR* 2.6 30.2 + - + -
2099B LYS* 4.0 5.2 + - + +
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Residues in contact with SER2096 (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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19A GLN* 4.1 11.8 - - - +
2092B GLY 3.1 12.9 + - - -
2093B ASP* 3.0 19.2 + - - -
2095B ILE* 1.3 77.1 - - - +
2097B ALA* 1.4 58.9 + - - +
2098B THR 3.5 0.3 + - - -
2099B LYS* 3.7 19.4 + - - +
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Residues in contact with ALA2097 (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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38A PRO* 3.7 20.4 - - - +
39A ASP 5.8 0.9 - - - +
40A LEU* 3.9 9.0 - - + +
43A PRO* 3.9 24.0 - - + -
2093B ASP 3.1 13.5 + - - +
2094B LEU 3.0 13.0 + - - +
2096B SER* 1.4 74.7 + - - +
2098B THR* 1.4 61.4 + - - +
2099B LYS 3.4 2.8 + - - +
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Residues in contact with THR2098 (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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23A LEU* 4.0 9.9 - - + +
35A LYS* 5.7 1.6 - - - -
36A ALA 4.9 0.7 - - - +
37A ILE* 3.9 25.0 - - - +
38A PRO* 3.4 18.1 - - - +
40A LEU* 3.8 24.9 - - + -
108A LEU* 4.3 18.4 - - + -
2094B LEU* 3.3 16.2 - - + +
2095B ILE* 2.6 22.6 + - + +
2097B ALA* 1.4 78.3 - - - +
2099B LYS* 1.3 80.1 + - - +
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Residues in contact with LYS2099 (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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23A LEU* 3.5 27.2 + - + +
26A MET* 4.8 20.1 - - + +
27A HIS* 6.4 0.4 - - - +
35A LYS* 3.8 28.5 - - - +
37A ILE* 5.5 8.6 - - - +
38A PRO* 5.4 4.1 - - - +
2095B ILE* 4.4 4.7 - - + +
2096B SER* 3.7 16.8 + - - +
2097B ALA 3.4 3.7 - - - +
2098B THR* 1.3 101.1 - - - +
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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
------------------------------------------------------------
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