Contacts of the helix formed by residues 141 - 145 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A PRO* 3.0 43.8 - - - +
218A ALA* 3.6 3.2 - - - +
129C GLY* 2.7 24.4 + - - +
131C LEU* 3.5 15.5 - - - +
140C HIS* 1.3 79.9 + - + +
142C LEU* 1.3 71.3 + - - +
144C CYS* 3.3 4.3 + - - +
145C ALA* 2.9 29.6 + - + +
152C ILE* 4.0 5.8 - - + +
153C ASP* 3.2 35.3 + - - +
156C LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO 3.8 20.0 - - - +
59C LEU* 3.6 38.5 - - + +
60C VAL 3.7 17.0 - - - +
61C LEU 4.0 3.1 - - - +
62C PRO* 3.7 36.6 - - + -
63C HIS* 5.0 9.0 + - - +
140C HIS* 2.8 18.7 + - + +
141C ARG* 1.3 92.2 - - - +
143C GLN* 1.3 64.1 + - - +
145C ALA* 4.1 17.3 + - + +
146C ARG* 4.9 8.7 + - - +
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Residues in contact with GLN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LYS 2.9 25.5 + - - +
56C PHE* 3.8 2.1 - - - -
57C GLN* 3.1 41.9 + - - +
59C LEU* 3.8 18.4 - - + -
74C GLN* 4.1 7.9 + - - -
139C LEU* 3.8 17.0 - - + +
140C HIS 2.6 32.8 + - - +
142C LEU* 1.3 71.2 - - - +
144C CYS* 1.3 63.3 + - - +
145C ALA 3.1 1.8 - - - -
146C ARG* 3.0 23.6 + - - +
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Residues in contact with CYS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C GLN* 3.9 11.0 - - - -
131C LEU* 3.4 23.3 - - + -
133C PHE* 3.9 22.4 - - - -
139C LEU* 3.5 28.7 - - - -
140C HIS 3.3 1.0 + - - -
141C ARG 3.6 7.6 - - - +
143C GLN* 1.3 72.8 - - - +
145C ALA* 1.3 59.9 + - - +
146C ARG 2.8 12.1 + - - -
147C GLY 3.1 1.6 + - - -
148C PHE* 2.9 29.1 + - + +
152C ILE* 3.6 20.9 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PRO* 6.4 0.2 - - + -
141C ARG* 2.9 17.1 + - + +
142C LEU* 4.1 22.0 - - + +
143C GLN 3.1 0.8 - - - -
144C CYS* 1.3 77.7 - - - +
146C ARG* 1.3 58.3 + - + +
149C GLY* 2.9 29.8 + - - +
152C ILE* 3.9 16.6 - - + -
153C ASP* 6.5 0.4 - - - -
241C ARG* 4.8 0.2 + - - -
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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