Contacts of the helix formed by residues 141 - 149 (chain A) in PDB entry 2QW4
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 ARG 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PRO 4.1 7.1 + - - -
128A GLU 5.7 0.4 - - - -
129A GLY* 2.8 44.1 + - - +
131A LEU* 3.7 12.2 - - - +
140A HIS* 1.3 83.3 + - + +
142A LEU* 1.3 80.3 + - + +
144A CYS* 2.9 18.4 + - - +
145A ALA* 3.0 13.6 + - + +
152A ILE* 4.1 7.0 - - + +
153A ASP* 3.9 19.1 - - - +
156A LEU* 3.6 27.3 - - + +
160A ARG* 5.1 6.3 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.7 33.6 - - + +
60A VAL* 4.0 6.1 - - - -
61A LEU 3.9 24.5 - - - +
62A PRO* 4.2 23.3 - - + -
63A HIS* 5.4 6.8 + - - +
140A HIS* 3.1 14.7 - - + +
141A ARG* 1.3 97.5 - - + +
143A GLN* 1.3 64.3 + - - +
144A CYS 3.1 1.1 - - - -
145A ALA* 4.0 17.6 + - + +
146A ARG* 4.4 8.1 + - - -
153A ASP* 5.8 0.9 - - - +
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Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS 2.8 27.5 + - - -
56A PHE* 3.9 0.9 - - - -
57A GLN* 2.9 50.7 + - - +
59A LEU* 4.1 10.0 - - + +
74A GLN* 5.4 4.6 - - - +
139A LEU* 4.2 17.0 - - + +
140A HIS* 2.9 31.5 + - + +
142A LEU* 1.3 79.6 - - - +
144A CYS* 1.3 58.8 + - - +
146A ARG* 3.3 25.7 - - - +
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.8 15.3 - - + -
133A PHE* 4.0 14.8 - - - -
139A LEU* 3.8 32.3 - - - -
140A HIS 2.8 12.9 + - - +
141A ARG 2.9 8.3 + - - +
143A GLN* 1.3 76.5 - - - +
145A ALA* 1.3 65.7 + - - +
146A ARG* 2.8 4.5 + - - -
147A GLY 3.2 2.6 + - - +
148A PHE* 3.0 32.1 + - + +
152A ILE* 3.9 22.0 - - + -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 3.0 13.4 + - + +
142A LEU* 4.2 15.5 - - + +
143A GLN 3.6 0.2 - - - -
144A CYS* 1.3 74.9 - - - +
146A ARG* 1.3 65.0 + - - +
149A GLY* 2.9 37.9 + - - +
150A ASP* 6.2 0.2 - - - +
152A ILE* 4.2 6.8 - - + +
153A ASP* 6.0 1.1 - - - +
241A ARG* 3.9 0.3 + - - -
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 2.9 53.2 + - - +
65A GLY* 4.0 22.4 + - - -
66A LYS 4.8 2.2 + - - -
67A GLU* 3.1 27.1 - - - +
68A ASP* 3.0 26.9 + - - -
71A ASP* 3.2 31.0 + - + +
142A LEU 4.4 5.3 + - - -
143A GLN* 3.3 21.3 + - - +
144A CYS 2.8 0.8 + - - -
145A ALA* 1.3 79.1 - - - +
147A GLY* 1.3 57.7 - - - +
241A ARG* 3.1 11.3 + - - -
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU* 4.9 2.2 - - - -
71A ASP* 4.3 22.3 - - - +
72A VAL* 5.1 2.7 - - - -
75A PHE* 3.2 22.6 - - - -
144A CYS* 3.2 3.2 + - - +
146A ARG* 1.3 78.0 - - - +
148A PHE* 1.3 61.2 + - - +
241A ARG* 2.7 27.9 + - - -
245A LEU* 4.1 3.4 - - - +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.3 40.4 - + + -
78A LEU* 4.4 19.7 - - + -
79A LEU* 5.1 0.7 - - + -
116A PHE* 4.0 23.1 - + - -
120A LEU* 5.2 0.4 - - + -
133A PHE* 4.0 22.4 - + - -
144A CYS* 3.0 22.7 + - + +
147A GLY* 1.3 80.3 - - - +
149A GLY* 1.3 58.2 + - - +
151A TRP* 3.0 56.8 - + - +
152A ILE* 3.8 35.9 - - + +
155A ILE* 4.7 3.8 - - + -
241A ARG* 3.5 12.7 - - - +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA* 2.9 26.8 + - - +
148A PHE* 1.3 80.3 - - - +
150A ASP* 1.3 65.3 + - - +
151A TRP 3.2 0.7 + - - -
152A ILE* 3.4 19.9 + - - +
153A ASP* 4.9 0.3 - - - +
241A ARG* 3.2 18.5 - - - +
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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