Contacts of the helix formed by residues 126 - 133 (chain B) in PDB entry 3QTH
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 ALA 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 5.2 1.9 - - - +
68B PRO* 4.9 13.7 - - + -
108B GLN 3.5 24.0 - - - +
109B LEU* 3.4 13.8 + - + +
111B LEU* 2.8 13.8 + - + +
113B VAL* 3.7 23.3 - - + -
124B MSE 3.3 1.2 + - - -
125B PRO* 1.4 67.8 - - - +
127B SER* 1.3 61.8 + - - +
129B TYR* 3.4 5.0 + - + +
130B MSE 3.0 24.4 + - - +
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Residues in contact with SER 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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10A LYS* 5.7 1.0 - - - -
4B ARG* 3.6 52.6 + - - +
7B LEU* 3.9 16.1 - - - +
8B TYR* 6.0 1.1 - - - +
109B LEU* 3.0 26.2 + - - +
125B PRO 3.0 0.2 + - - -
126B ALA* 1.3 76.3 - - - +
128B GLU* 1.4 61.4 + - - +
130B MSE 3.3 5.0 + - - +
131B SER* 3.2 25.1 + - - -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 4.9 12.5 - - - +
4B ARG* 2.8 46.0 + - - -
124B MSE 3.4 16.2 - - + +
125B PRO* 3.0 26.7 + - + +
127B SER* 1.4 71.4 - - - +
129B TYR* 1.3 60.4 + - - +
131B SER* 5.1 2.0 - - - -
132B SER* 2.8 45.9 + - - +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 3.4 42.1 + - - +
65B ALA* 4.4 4.9 - - - -
68B PRO* 4.5 2.7 - - + -
113B VAL* 3.7 38.4 - - + +
115B ASP* 2.6 38.7 + - + -
122B ILE* 4.3 2.9 - - + -
124B MSE 3.9 27.5 - - + +
125B PRO 2.9 12.4 + - - +
126B ALA* 3.4 14.4 - - - +
128B GLU* 1.3 76.5 - - - +
130B MSE 1.4 59.4 + - - +
133B PHE* 3.3 24.3 + + - +
134B VAL* 2.9 43.2 + - + +
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Residues in contact with MSE 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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8B TYR* 3.4 59.9 - - + +
11B HIS* 3.9 15.7 - - + -
12B ARG 4.2 5.6 - - - +
15B PHE* 3.5 22.6 - - + -
65B ALA* 3.8 18.4 - - + +
66B CYS* 3.7 26.5 - - - -
126B ALA 3.0 16.1 + - - +
127B SER* 3.7 5.6 - - - +
128B GLU 3.2 0.4 - - - -
129B TYR* 1.4 78.8 - - - +
131B SER* 1.3 61.6 + - - +
134B VAL* 3.6 7.6 - - - +
135B LEU* 2.9 29.3 + - - +
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Residues in contact with SER 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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10A LYS* 3.9 23.6 - - - -
14A ILE* 4.1 10.9 - - - +
7B LEU* 3.6 12.0 - - - +
11B HIS* 2.6 39.6 + - - +
127B SER 3.2 12.8 + - - -
130B MSE 1.3 81.4 - - - +
132B SER* 1.3 62.2 + - - +
135B LEU* 3.4 21.0 - - - +
136B PRO* 3.8 4.7 - - - +
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Residues in contact with SER 132 (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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10A LYS* 3.2 21.9 + - - +
14A ILE* 5.2 3.6 - - - +
17A LYS* 4.3 12.3 + - - +
18A HIS* 4.9 1.6 + - - -
162A ASP* 5.1 1.6 - - - +
164A ILE* 3.6 16.1 - - - +
124B MSE 4.0 13.0 - - - -
128B GLU* 2.8 27.9 + - - +
131B SER* 1.3 73.3 - - - +
133B PHE* 1.3 57.2 + - - +
136B PRO* 3.5 17.3 - - - +
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Residues in contact with PHE 133 (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 ASP* 3.8 7.6 - - - -
164A ILE* 3.7 20.4 - - + -
165A HIS* 3.4 37.0 - + - -
61B PHE* 4.1 10.1 - + - -
64B ARG* 3.8 15.9 - - - -
115B ASP* 3.8 20.9 - - - -
116B THR 4.5 0.9 - - - -
117B ALA* 3.7 21.1 - - + -
122B ILE* 4.0 7.9 - - + -
124B MSE 3.9 18.8 - - - -
128B GLU 3.5 0.2 + - - -
129B TYR* 3.3 31.7 + + - +
132B SER* 1.3 79.7 - - - +
134B VAL* 1.3 70.3 + - + +
136B PRO* 3.5 5.8 - - - +
137B ASN* 2.7 29.2 + - - -
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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