Contacts of the helix formed by residues 106 - 118 (chain B) in PDB entry 2HXO
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 TRP 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.3 6.7 - - + -
28B LEU* 3.3 67.1 - - + +
29B ASP* 2.7 24.8 + - - -
32B GLY* 5.6 1.3 - - - -
33B GLU* 5.4 7.6 - - + +
63B LEU 5.0 0.4 - - - -
66B ALA* 3.9 21.5 - - + -
67B THR* 3.8 25.1 - - - -
70B VAL* 3.9 12.1 - - + -
104B HIS* 3.3 29.0 - + + +
105B PRO* 1.3 78.6 - - + +
107B LEU* 1.3 86.5 + - + +
108B ALA 3.3 0.2 - - - -
109B THR* 3.2 20.3 + - - -
110B GLN* 3.3 27.1 + - + +
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Residues in contact with LEU 107 (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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67B THR* 3.5 45.8 - - + +
70B VAL* 3.9 10.8 - - + -
71B VAL* 4.2 12.1 - - + -
97B LEU* 5.5 0.4 - - + -
100B ALA* 3.6 35.7 - - + +
101B THR* 3.6 19.3 - - + -
104B HIS* 2.8 22.5 + - + +
106B TRP* 1.3 95.0 - - + +
108B ALA* 1.3 63.5 + - - +
110B GLN* 3.2 2.5 + - - +
111B LEU* 3.0 28.5 + - + +
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Residues in contact with ALA 108 (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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101B THR* 4.3 13.0 - - + +
104B HIS 4.4 0.2 + - - -
105B PRO 3.5 5.1 + - - +
106B TRP 3.3 0.8 - - - -
107B LEU* 1.3 78.6 - - - +
109B THR* 1.3 62.0 + - - +
111B LEU* 3.4 8.8 + - - +
112B ALA* 3.3 20.3 + - - +
157B LEU* 5.0 3.4 - - - +
160B ALA 5.3 0.2 - - - -
161B GLY* 4.4 17.0 - - - +
164B ALA* 3.9 27.8 - - + -
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Residues in contact with THR 109 (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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33B GLU* 5.5 2.2 - - - +
105B PRO 4.6 3.3 + - - -
106B TRP* 3.2 13.7 + - - -
108B ALA* 1.3 78.3 - - - +
110B GLN* 1.3 74.0 + - - +
112B ALA* 3.3 7.9 + - + +
113B THR* 3.1 30.4 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 3.2 28.1 + - - +
63B LEU* 4.0 33.6 - - + +
67B THR* 3.2 26.0 + - + +
106B TRP* 3.3 25.9 + - + +
107B LEU 3.2 8.4 + - - +
109B THR* 1.3 89.1 - - - +
111B LEU* 1.3 59.0 + - - +
113B THR* 3.4 16.4 + - - +
114B GLN* 2.8 36.5 + - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 3.7 22.2 - - + -
71B VAL* 4.3 4.9 - - + -
97B LEU* 4.4 16.2 - - + -
101B THR* 4.3 14.4 - - + -
107B LEU* 3.0 32.1 + - + +
108B ALA* 3.7 9.0 - - - +
109B THR 3.2 0.4 - - - -
110B GLN* 1.3 73.9 - - - +
112B ALA* 1.3 65.9 + - - +
114B GLN* 3.3 5.5 + - + +
115B LEU* 3.0 33.8 + - + +
123B VAL* 4.0 20.4 - - + -
127B ILE* 4.6 8.1 - - + -
157B LEU* 3.9 27.4 - - + -
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Residues in contact with ALA 112 (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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161A GLY 6.1 0.4 - - - +
162A GLN* 3.1 25.3 + - - +
165A ALA* 4.9 7.9 - - + -
108B ALA 3.3 8.9 + - - +
109B THR* 3.3 12.0 + - + +
110B GLN 3.3 0.4 - - - -
111B LEU* 1.3 78.0 - - - +
113B THR* 1.3 56.4 + - - +
116B SER* 2.5 34.2 + - - +
117B ARG* 4.5 2.9 - - - +
157B LEU* 4.6 4.4 - - + +
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Residues in contact with THR 113 (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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109B THR* 3.1 18.5 + - - +
110B GLN* 3.7 21.9 + - - +
112B ALA* 1.3 75.2 - - - +
114B GLN* 1.3 60.4 + - - +
117B ARG* 3.0 58.4 + - + +
118B THR* 3.3 10.8 + - - +
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Residues in contact with GLN 114 (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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182A PHE* 4.7 0.7 - - - -
64B GLY* 4.1 22.9 - - - +
67B THR* 4.8 6.7 + - + -
110B GLN* 2.8 24.1 + - - +
111B LEU* 3.4 12.8 - - + +
112B ALA 3.2 0.2 - - - -
113B THR* 1.3 80.0 - - - +
115B LEU* 1.3 64.8 + - + +
118B THR* 3.3 42.9 + - - +
121B GLY* 3.2 29.8 - - - -
122B THR 4.0 2.4 + - - -
123B VAL* 4.0 30.5 - - + +
124B ALA* 4.7 9.2 - - + +
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Residues in contact with LEU 115 (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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162A GLN* 3.2 32.0 + - + +
166A ASN* 3.4 4.9 + - - +
182A PHE* 3.2 22.7 - - - -
111B LEU* 3.0 18.1 + - + +
113B THR 3.3 0.2 - - - -
114B GLN* 1.3 79.9 - - + +
116B SER* 1.3 57.2 + - - +
124B ALA* 3.3 37.7 - - + +
127B ILE* 6.2 2.9 - - + -
153B MSE 4.6 21.8 - - + -
154B HIS* 5.7 4.9 - - + -
157B LEU* 4.4 22.4 - - + -
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Residues in contact with SER 116 (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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162A GLN* 2.5 25.8 + - - -
165A ALA* 3.0 20.3 - - - +
166A ASN* 3.2 33.1 + - - +
182A PHE* 3.7 18.4 - - - +
112B ALA 2.5 12.8 + - - -
115B LEU* 1.3 78.8 - - - +
117B ARG* 1.3 80.3 + - - +
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Residues in contact with ARG 117 (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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165A ALA* 3.4 36.1 + - - +
166A ASN* 5.6 0.2 - - + -
182A PHE* 3.9 3.8 - - - -
112B ALA* 5.4 1.4 - - - +
113B THR* 3.0 49.3 + - + +
116B SER* 1.3 92.3 - - - +
118B THR* 1.3 62.7 + - - +
119B PRO* 3.1 14.8 - - - +
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Residues in contact with THR 118 (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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182A PHE* 3.7 3.9 - - - -
113B THR* 3.3 17.8 + - - +
114B GLN* 3.3 50.7 + - - +
117B ARG* 1.3 79.1 + - - +
119B PRO* 1.3 58.2 - - + +
120B TRP* 4.4 2.7 - - + +
121B GLY* 2.9 28.5 + - - +
124B ALA* 5.9 1.4 - - - +
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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