Contacts of the helix formed by residues 119 - 133 (chain D) in PDB entry 4MDK
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 ASN 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLU* 3.3 18.4 - - - +
68D TYR* 3.5 11.2 - - - -
117D THR 4.7 4.4 + - - -
118D GLN* 1.3 79.9 - - - +
120D VAL* 1.3 63.0 + - - +
121D ARG* 4.0 14.3 - - + +
122D THR* 2.1 68.9 + - - +
123D ILE* 3.3 16.9 + - - +
8H LEU 5.2 6.3 + - - -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 5.0 0.7 - - + -
16D GLU* 2.9 17.4 + - + +
20D LEU* 3.8 21.8 - - + -
30D VAL* 5.4 0.7 - - + -
41D TRP* 3.9 18.8 - - + -
62D LEU* 4.1 11.7 - - + -
64D PHE* 3.8 31.2 - - + -
68D TYR* 3.8 5.6 - - + +
119D ASN* 1.3 73.0 - - - +
121D ARG* 1.3 66.3 + - - +
123D ILE* 3.3 11.4 + - + +
124D LEU* 3.1 40.7 + - + +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLU* 4.4 1.2 + - - -
19D GLY* 3.2 21.6 + - - -
20D LEU* 3.3 23.1 - - + +
23D GLU* 3.0 47.6 + - - -
24D PRO 4.2 2.2 + - - -
25D VAL* 3.5 30.9 - - + +
119D ASN* 3.2 15.3 - - + +
120D VAL* 1.3 79.3 - - - +
122D THR* 1.3 62.4 + - + +
124D LEU* 3.5 3.7 + - - +
125D LEU* 3.1 35.1 + - + +
6H LYS* 6.3 3.1 - - - -
68H HIS* 5.7 9.2 - - - -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLN* 3.7 15.0 - - + +
119D ASN* 2.1 56.5 + - - +
121D ARG* 1.3 72.8 - - + +
123D ILE* 1.3 60.1 + - - +
125D LEU* 3.2 8.7 + - + +
126D SER* 2.8 33.0 + - - -
8H LEU* 3.3 45.1 - - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 4.7 13.9 - - + -
68D TYR* 5.9 0.4 - - + -
73D PRO* 3.4 38.8 - - + +
75D PHE* 4.7 8.7 - - + -
118D GLN* 6.1 3.4 - - + -
119D ASN 3.5 15.3 - - - +
120D VAL* 3.3 15.4 + - + +
122D THR* 1.3 77.6 - - - +
124D LEU* 1.3 74.1 + - + +
126D SER* 3.1 9.7 + - - -
127D VAL* 3.0 32.9 + - + +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.7 9.9 - - + -
25D VAL* 4.4 22.4 - - + -
28D PHE* 3.4 41.5 - - + -
30D VAL* 5.2 10.3 - - + -
43D VAL* 5.4 2.2 - - + -
62D LEU* 4.5 11.9 - - + -
75D PHE* 4.7 8.7 - - + -
120D VAL* 3.1 39.0 + - + +
121D ARG 3.7 4.3 - - - +
123D ILE* 1.3 90.0 - - + +
125D LEU* 1.3 57.3 + - - +
127D VAL* 3.6 8.5 + - - +
128D ILE* 3.2 32.6 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 4.3 21.5 - - + -
26D GLU* 5.4 1.3 - - - +
121D ARG* 3.1 35.4 + - + +
122D THR* 3.7 8.5 - - + +
123D ILE 3.1 0.6 - - - -
124D LEU* 1.3 76.3 - - - +
126D SER* 1.3 64.6 + - - +
128D ILE* 3.3 11.0 + - + +
129D SER* 3.1 21.1 + - - -
8H LEU* 4.9 10.8 - - + -
44H ILE* 3.9 27.7 - - + +
68H HIS* 4.3 36.3 - - + +
69H LEU 5.8 0.7 - - - +
70H VAL* 4.2 16.1 - - + +
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D CYS* 5.6 10.5 - - - -
122D THR* 2.8 20.1 + - - -
123D ILE* 3.3 11.2 - - - -
125D LEU* 1.3 74.8 - - - +
127D VAL* 1.3 60.4 + - - +
129D SER* 3.0 11.6 + - - -
130D LEU* 2.9 32.6 + - - +
70H VAL* 5.0 5.2 - - - +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 4.2 15.0 - - + -
45D ILE* 5.8 0.9 - - + -
75D PHE* 4.4 31.6 - - + -
77D PHE* 4.9 6.1 - - + -
92D VAL* 5.4 9.9 - - + -
93D CYS* 6.2 3.1 - - - -
123D ILE* 3.0 28.1 + - + +
124D LEU* 3.6 11.0 - - - +
126D SER* 1.3 77.5 - - - +
128D ILE* 1.3 61.3 + - - +
130D LEU* 3.1 7.6 + - + +
131D LEU* 3.0 47.5 + - + +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 3.9 19.5 - - + -
26D GLU* 4.4 6.3 - - - +
28D PHE* 3.5 30.3 - - + -
124D LEU 3.2 13.8 + - - +
125D LEU* 3.6 16.6 - - + +
126D SER 3.2 0.2 - - - -
127D VAL* 1.3 77.0 - - - +
129D SER* 1.3 58.5 + - - +
131D LEU* 3.6 6.5 + - + +
132D ASN* 2.9 40.0 + - - +
201D U94 4.0 13.2 - - + -
44H ILE* 4.1 19.1 - - + -
47H GLY* 3.6 33.2 - - - +
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Residues in contact with SER 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU 3.1 11.2 + - - -
126D SER* 3.0 11.6 + - - -
128D ILE* 1.3 79.5 - - - +
130D LEU* 1.3 56.9 + - - +
132D ASN* 3.8 0.5 - - - +
133D GLU* 2.9 30.3 + - - +
44H ILE* 4.7 3.1 - - - -
49H GLN* 2.8 29.4 + - - -
70H VAL* 4.1 17.5 - - - +
72H ARG* 3.2 27.2 + - - -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D HIS* 3.1 19.2 + - + -
85D ASN* 3.9 32.8 - - + +
92D VAL* 4.4 20.9 - - + -
93D CYS* 5.0 11.4 - - + -
126D SER* 2.9 14.7 + - - +
127D VAL* 3.1 12.3 + - - +
129D SER* 1.3 76.5 - - - +
131D LEU* 1.3 67.0 + - + +
133D GLU 3.8 1.3 - - - +
134D PRO* 3.2 17.2 - - - +
135D ASN* 4.7 6.3 - - + +
72H ARG* 3.3 28.7 - - - +
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 5.4 1.3 - - + -
45D ILE* 5.1 4.9 - - + -
53D TYR* 4.6 12.7 + - + -
77D PHE* 4.8 17.3 - - + -
83D HIS* 3.8 24.1 + - + +
86D ILE* 4.9 8.3 - - + -
127D VAL* 3.0 40.2 + - + +
128D ILE* 3.8 5.6 - - - +
130D LEU* 1.3 81.8 - - + +
132D ASN* 1.3 61.6 + - - +
134D PRO* 4.6 3.5 - - - +
201D U94 3.3 66.3 + - + +
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Residues in contact with ASN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 2.9 30.5 + - - +
129D SER 3.8 3.8 - - - +
131D LEU* 1.3 77.5 - - - +
133D GLU* 1.3 59.3 + - - +
134D PRO* 3.9 4.8 - - - +
148D TYR* 4.2 7.1 + - - -
152D LYS* 5.5 0.9 + - - -
201D U94 3.3 58.4 + - + +
47H GLY 3.4 12.1 + - - -
48H LYS* 3.8 1.6 - - - +
49H GLN* 3.0 45.5 + - + +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D SER 2.9 9.3 + - - +
130D LEU 3.3 3.1 - - - +
132D ASN* 1.3 78.9 - - - +
134D PRO* 1.3 62.6 - - + +
152D LYS* 4.9 11.9 - - - +
42H ARG* 3.0 38.9 + - - -
49H GLN* 3.3 15.6 + - - +
72H ARG* 2.6 59.9 + - - +
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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