Contacts of the helix formed by residues 120 - 131 (chain B) in PDB entry 2HUE
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 MET 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B ARG* 3.6 25.6 - - - +
118B THR* 4.0 11.9 - - - +
119B ILE* 1.3 76.5 - - - +
121B PRO* 1.3 83.3 - - + +
122B LYS* 4.0 15.9 - - + +
123B ASP* 2.7 25.7 + - - +
124B ILE* 3.3 4.3 + - - +
47C SER* 3.8 20.0 - - - +
49C LEU* 5.4 5.6 - - + -
50C ILE* 3.5 9.3 - - - +
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Residues in contact with PRO 121 (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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120B MET* 1.3 93.2 - - + +
122B LYS* 1.3 62.4 + - - +
124B ILE* 3.1 6.0 + - - +
125B GLN* 3.1 24.9 + - - +
47C SER* 4.1 13.9 - - - +
49C LEU* 3.5 39.9 - - + +
50C ILE* 3.7 7.2 - - + -
53C GLU* 3.7 31.1 - - + +
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Residues in contact with LYS 122 (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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48A SER* 3.5 23.6 - - - +
88A GLU* 6.0 1.2 - - - +
91A SER* 3.0 19.4 + - - -
92A VAL* 2.9 38.4 + - - +
116B ARG* 4.1 3.1 - - - +
120B MET* 3.1 15.0 + - + +
121B PRO* 1.3 78.2 - - - +
123B ASP* 1.3 64.9 + - - +
125B GLN* 3.3 2.7 + - - +
126B LEU* 2.8 46.7 + - - +
402B SO4 2.9 29.7 + - - +
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Residues in contact with ASP 123 (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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92A VAL* 4.4 0.2 - - - +
107B THR* 3.5 28.7 + - + +
110B CYS* 3.4 22.7 - - + +
111B ALA* 3.8 9.7 + - - +
116B ARG* 2.7 46.6 + - - -
119B ILE* 3.4 4.0 - - - -
120B MET* 2.7 26.5 + - - +
122B LYS* 1.3 79.8 - - - +
124B ILE* 1.3 57.4 + - - +
126B LEU* 3.4 1.4 + - - +
127B ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.0 16.8 - - + +
104B PHE* 4.3 8.7 - - + -
107B THR* 3.6 26.5 - - + +
120B MET 3.3 0.6 + - - -
121B PRO 3.1 8.1 + - - +
123B ASP* 1.3 74.6 - - - +
125B GLN* 1.3 66.4 + - - +
127B ALA* 3.2 3.3 + - - +
128B ARG* 3.0 21.7 + - - +
50C ILE* 3.5 30.7 - - + -
53C GLU* 4.0 18.6 - - + -
54C THR* 3.6 23.8 - - - +
57C VAL* 3.7 29.8 - - + -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 3.4 29.9 - - - +
49A ARG* 5.7 1.3 - - - -
121B PRO 3.1 10.1 + - - +
122B LYS* 3.9 6.3 - - - +
124B ILE* 1.3 75.2 - - - +
126B LEU* 1.3 64.7 + - - +
128B ARG* 3.0 46.3 + - - +
129B ARG* 3.0 18.0 + - + +
53C GLU* 2.5 34.4 + - - +
57C VAL* 3.8 13.3 - - - +
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Residues in contact with LEU 126 (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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45A VAL* 4.1 6.1 - - + -
48A SER* 3.7 24.2 - - - +
92A VAL 3.6 22.9 - - - +
93A THR* 3.8 25.1 - - - +
94A VAL* 3.9 25.4 - - + +
112A TYR* 4.4 2.2 - - - -
110B CYS* 3.7 26.5 - - - -
122B LYS* 2.8 33.4 + - - +
123B ASP 3.9 2.9 - - - +
125B GLN* 1.3 77.3 - - - +
127B ALA* 1.3 50.9 + - - +
129B ARG* 2.9 7.6 + - + +
130B ILE* 2.7 35.3 + - - +
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Residues in contact with ALA 127 (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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112A TYR* 3.5 14.3 + - - +
103B LEU* 3.6 13.9 - - + -
106B ASP* 3.6 19.5 - - + -
107B THR* 3.5 17.5 - - - +
123B ASP 2.9 19.3 + - - +
124B ILE 3.2 6.0 + - - +
126B LEU* 1.3 75.8 - - - +
128B ARG* 1.3 62.0 + - - +
130B ILE* 3.9 1.8 - - - -
131B ARG* 3.1 31.4 + - - +
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Residues in contact with ARG 128 (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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99B TYR* 4.2 8.4 + - - +
103B LEU* 3.9 15.7 - - + -
124B ILE 3.0 16.5 + - - +
125B GLN* 3.0 40.5 + - - +
127B ALA* 1.3 76.3 - - - +
129B ARG* 1.3 59.6 + - + +
131B ARG* 4.5 2.9 - - - +
132B GLY 3.8 1.9 + - - -
133B GLU* 2.9 44.3 + - + -
56C GLY 5.8 0.4 - - - -
57C VAL* 3.6 40.2 + - + +
60C VAL* 3.6 35.2 - - - +
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Residues in contact with ARG 129 (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 THR* 5.1 0.4 - - - +
45A VAL* 3.6 23.4 - - + +
47A SER 4.9 1.2 + - - -
48A SER* 5.9 4.3 - - - +
50A SER 4.8 1.4 + - - -
51A LEU* 3.8 32.2 - - - +
54A ASP* 2.7 43.0 + - - -
94A VAL* 3.9 15.9 - - + -
96A LEU* 3.2 40.9 - - + +
108A ARG* 4.4 4.9 + - - +
125B GLN* 3.0 18.4 + - + +
126B LEU* 2.9 12.3 + - + +
128B ARG* 1.3 76.9 - - - +
130B ILE* 1.3 63.8 + - - +
131B ARG 3.2 0.4 - - - -
132B GLY* 3.2 12.8 + - - -
133B GLU* 3.3 30.6 + - - +
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Residues in contact with ILE 130 (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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94A VAL* 4.1 6.4 - - + +
96A LEU* 4.4 5.1 - - - +
108A ARG* 5.3 1.7 - - - +
110A GLY* 3.4 30.1 + - - +
111A TYR* 3.8 3.1 - - - +
112A TYR* 3.2 63.9 - - + +
143A LYS 4.9 0.9 - - - +
145A ARG* 3.1 48.8 - - + +
106B ASP* 4.1 4.9 - - - -
126B LEU 2.7 16.0 + - - +
127B ALA* 3.2 9.8 + - - +
129B ARG* 1.3 72.1 - - - +
131B ARG* 1.4 67.7 + - + +
132B GLY 3.7 0.3 + - - -
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Residues in contact with ARG 131 (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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108A ARG* 4.9 0.2 - - - -
145A ARG* 5.6 0.2 - - + -
147A THR* 2.5 31.3 + - - +
99B TYR* 4.9 17.7 + - - +
102B ALA* 3.6 34.2 + - - +
103B LEU* 3.9 24.8 - - - +
106B ASP* 2.5 55.0 + - - +
127B ALA 3.1 17.1 + - - +
128B ARG* 4.7 3.6 - - - +
130B ILE* 1.4 76.9 - - + +
132B GLY* 1.3 56.7 + - - +
133B GLU 3.9 0.7 - - - -
93C GLN* 5.1 7.1 - - - +
96C THR* 3.2 39.1 + - + +
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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
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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