Contacts of the helix formed by residues 138 - 143 (chain A) in PDB entry 4QG0
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 THR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A ARG 3.5 15.7 - - - +
135A ILE 3.0 16.3 + - - +
136A ILE 2.8 5.7 + - - -
137A ASP* 1.3 79.7 - - - +
139A PRO* 1.3 70.3 - - - +
140A GLN* 3.7 2.2 + - - -
141A PHE 3.2 13.0 + - - -
142A GLN* 2.9 31.7 + - - +
244A LEU* 3.4 15.4 - - + +
248A ASN* 3.5 36.8 - - + +
250A ILE* 4.9 0.7 - - + -
449D GLU 3.9 4.0 + - - -
450D TYR* 5.7 0.2 - - + -
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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 THR* 1.3 88.6 - - - +
140A GLN* 1.3 74.0 + - - +
142A GLN* 4.2 0.2 - - - +
143A ARG* 2.9 31.9 + - - +
248A ASN* 3.9 3.1 - - - +
420A THR* 4.1 13.2 - - + +
446D LYS* 6.3 0.4 - - - +
449D GLU* 3.4 33.3 - - + +
450D TYR* 3.7 40.4 - - + +
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Residues in contact with GLN 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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138A THR* 3.1 0.5 - - - -
139A PRO* 1.3 93.2 - - - +
141A PHE* 1.3 59.0 + - - +
143A ARG* 3.7 14.8 - - - +
144A LEU* 4.7 2.1 - - - +
208A LEU* 3.7 13.9 - - - +
240A MET* 3.6 32.0 - - + +
243A HIS* 3.7 24.8 + - + -
244A LEU* 3.8 28.9 - - + -
247A SER* 4.6 3.8 - - - -
248A ASN* 3.0 27.7 + - - -
420A THR* 3.5 27.3 + - - +
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Residues in contact with PHE 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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135A ILE* 3.6 11.0 - - + +
136A ILE* 3.4 35.4 - - + +
138A THR* 3.2 14.5 + - - +
140A GLN* 1.3 72.7 - - - +
142A GLN* 1.3 67.4 + - - +
143A ARG 3.1 1.8 - - - -
144A LEU* 3.1 23.0 + - + +
165A PHE* 3.6 37.3 - + - -
168A SER* 3.8 15.9 - - - -
169A LEU* 4.3 5.6 - - + -
204A LEU* 3.3 52.9 - - + -
205A CYS* 4.5 8.5 - - - -
208A LEU* 3.8 20.2 - - + -
244A LEU* 4.2 2.4 - - + +
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Residues in contact with GLN 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 ILE* 3.1 22.4 + - - +
137A ASP* 4.0 3.9 + - - -
138A THR 2.9 20.8 + - - +
139A PRO 4.2 0.2 - - - +
141A PHE* 1.3 75.7 - - - +
143A ARG* 1.3 62.6 + - - +
145A ARG* 2.7 55.0 + - - +
146A TYR* 3.6 9.4 - - + +
165A PHE* 3.4 16.9 - - - -
155D TYR* 4.7 6.1 - - - -
448D ILE 5.6 1.2 - - - +
449D GLU* 3.8 39.5 - - + +
451D ARG* 5.5 2.1 + - - -
702D DGT 2.9 24.7 + - - -
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Residues in contact with ARG 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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139A PRO 2.9 18.5 + - - +
140A GLN* 3.7 13.0 + - - +
142A GLN* 1.3 75.6 - - - +
144A LEU* 1.3 63.0 + - - +
145A ARG 3.1 0.4 - - - -
146A TYR* 2.9 35.2 + - - +
147A ILE* 3.5 13.2 + - + +
208A LEU 3.4 20.6 + - - -
210A HIS 2.9 29.4 + - - -
211A GLY* 3.8 2.6 - - - -
240A MET* 4.9 6.0 - - - +
419A TYR* 2.9 43.2 + - - -
420A THR* 3.3 31.1 + - - +
422A LEU 2.9 23.9 + - - -
423A THR* 3.7 11.4 - - + +
432D TYR* 5.9 0.4 - - - -
449D GLU* 4.8 2.4 + - - -
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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