Contacts of the helix formed by residues 138 - 146 (chain A) in PDB entry 4H27
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 ASP 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.5 22.2 - - - -
52A TRP* 5.3 0.5 + - - -
134A PRO* 4.1 8.6 - - + +
136A PHE 3.1 3.2 + - - -
137A ASP* 1.3 77.9 - - - +
139A PRO* 1.3 79.9 - - - +
140A LEU* 2.8 38.8 + - - +
141A ILE* 2.9 32.8 + - + +
142A TRP* 3.2 16.8 + - - +
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Residues in contact with PRO 139 (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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138A ASP* 1.3 92.7 - - - +
140A LEU* 1.3 58.0 + - + +
142A TRP* 3.3 35.9 + - + +
143A GLU* 2.9 29.6 + - - +
178A GLN* 5.3 1.0 + - - -
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Residues in contact with LEU 140 (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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44A GLY 3.9 2.2 - - - +
47A HIS* 3.2 29.1 - - + +
48A PHE* 4.0 20.4 - - + -
51A ARG* 3.6 56.1 - - + +
52A TRP* 3.9 26.2 - - + +
138A ASP* 2.8 22.3 + - - +
139A PRO* 1.3 73.9 - - + +
141A ILE* 1.3 58.5 + - - +
143A GLU* 4.0 6.7 - - - +
144A GLY* 2.9 23.2 + - - -
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Residues in contact with ILE 141 (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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44A GLY* 3.3 22.5 - - - +
45A ILE* 4.5 7.6 - - + +
48A PHE* 4.2 11.7 - - + -
133A ILE* 5.5 0.2 - - + -
134A PRO* 3.3 44.9 - - + +
135A PRO 4.2 3.1 - - - +
136A PHE* 3.8 30.7 - - - +
138A ASP* 2.9 15.7 + - + +
140A LEU* 1.3 74.7 - - - +
142A TRP* 1.3 65.6 + - + +
144A GLY 3.3 0.2 + - - -
145A HIS* 2.9 51.7 + - + +
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Residues in contact with TRP 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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136A PHE* 2.9 25.4 + - - -
137A ASP* 3.4 24.6 - - - +
138A ASP 3.2 16.9 + - - -
139A PRO* 3.3 35.0 + - + +
141A ILE* 1.3 75.3 - - - +
143A GLU* 1.3 63.5 + - - +
145A HIS* 3.3 1.1 + - - -
146A ALA* 3.0 20.1 + - - +
171A GLY* 3.9 14.0 - - - -
174A CYS* 3.7 28.1 - - + +
175A GLY* 3.2 17.1 - - - +
178A GLN* 3.8 24.9 - - - +
231A GLN* 3.4 48.0 - - + -
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Residues in contact with GLU 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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47A HIS* 2.8 31.6 + - + +
51A ARG* 4.5 6.1 + - - -
139A PRO 2.9 16.8 + - - +
140A LEU* 3.7 15.4 - - - +
142A TRP* 1.3 77.0 - - - +
144A GLY* 1.3 64.4 + - - +
146A ALA* 3.3 18.5 + - - +
147A SER* 3.9 3.1 + - - -
178A GLN* 4.6 5.3 - - - +
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Residues in contact with GLY 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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8A HIS* 4.9 1.6 - - - -
43A ARG* 3.5 15.5 - - - +
44A GLY* 3.9 0.2 - - - -
47A HIS* 3.6 29.1 - - - -
140A LEU 2.9 12.1 + - - -
141A ILE 3.8 2.0 - - - -
143A GLU* 1.3 77.3 - - - +
145A HIS* 1.3 55.1 + - - +
147A SER* 2.7 33.0 + - - -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.5 31.4 - + - -
41A LLP 3.8 17.2 + - + +
43A ARG* 3.7 11.4 - - - +
44A GLY* 2.9 33.3 + - - -
45A ILE* 4.5 0.9 - - + -
135A PRO 5.2 3.2 + - - -
141A ILE* 2.9 35.1 + - + +
142A TRP 3.7 4.3 - - - +
144A GLY* 1.3 75.8 - - - +
146A ALA* 1.3 62.3 + - - +
147A SER 3.0 0.2 - - - -
148A ILE* 3.0 27.5 + - - +
171A GLY 3.4 28.7 - - - +
172A LEU* 3.5 15.6 + - + +
175A GLY* 4.0 11.4 - - - -
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Residues in contact with ALA 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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142A TRP 3.0 11.2 + - - +
143A GLU* 3.5 14.6 - - - +
144A GLY 3.2 1.0 - - - -
145A HIS* 1.3 74.7 - - - +
147A SER* 1.3 62.6 + - - +
148A ILE* 3.0 0.7 - - - -
149A VAL* 3.0 18.5 + - - +
150A LYS* 3.4 17.7 + - - +
175A GLY* 3.2 25.5 - - - +
178A GLN* 4.7 4.5 - - + -
179A GLY* 3.9 14.2 - - - +
182A GLU* 5.9 2.0 - - - +
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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