Contacts of the helix formed by residues 137 - 146 (chain S) in PDB entry 6O81
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 GLY 137 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135S CYS* 3.1 14.7 + - - +
136S PRO* 1.3 76.9 - - - +
138S HIS* 1.3 64.7 + - - -
139S ASP* 3.2 5.1 + - - -
140S ILE* 3.6 9.6 + - - +
141S LEU 3.8 6.4 + - - -
450S HIS* 6.3 3.4 - - - -
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Residues in contact with HIS 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S ILE* 4.3 22.0 - - + +
48S GLY 5.1 9.6 - - - +
135S CYS 5.3 0.2 - - - -
137S GLY* 1.3 71.4 - - - -
139S ASP* 1.3 59.9 + - - +
140S ILE 3.3 0.2 - - - -
141S LEU* 3.5 8.0 + - - +
142S MET* 2.9 30.0 + - - +
170S THR 5.6 1.3 - - - +
171S SER* 5.4 5.6 - - - -
174S LEU* 4.4 14.1 - - + +
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Residues in contact with ASP 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137S GLY* 3.2 1.7 - - - -
138S HIS* 1.3 76.2 - - - +
140S ILE* 1.3 60.7 + - - +
142S MET* 3.4 6.7 + - - +
143S ALA* 2.9 30.3 + - - +
174S LEU* 6.0 0.4 - - - -
451S TRP 3.6 21.8 - - - +
452S ARG* 3.8 22.9 - - + -
453S LEU* 4.0 11.0 - - + +
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Residues in contact with ILE 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S THR 4.1 19.7 - - - +
79S ILE* 4.9 10.1 - - - +
135S CYS* 5.0 7.0 - - + -
136S PRO 4.6 2.5 - - - +
137S GLY 3.6 9.8 + - - +
138S HIS 3.3 0.2 - - - -
139S ASP* 1.3 80.3 - - - +
141S LEU* 1.3 56.4 + - - +
143S ALA* 3.4 5.9 + - - +
144S THR* 2.9 29.3 + - - -
451S TRP* 4.7 6.3 + - + +
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Residues in contact with LEU 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S THR 5.3 4.0 - - - +
47S ILE* 5.0 12.8 - - + -
133S VAL 6.1 1.1 - - - +
135S CYS* 3.8 23.0 - - + +
137S GLY 3.8 5.1 + - - +
138S HIS* 3.5 10.4 + - - +
139S ASP 3.4 0.2 - - - -
140S ILE* 1.3 78.5 - - - +
142S MET* 1.3 58.7 + - - +
144S THR* 3.4 5.9 + - - -
145S MET* 2.9 30.7 + - - +
152S MET* 5.7 0.5 - - - +
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Residues in contact with MET 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138S HIS 2.9 19.0 + - - +
139S ASP* 3.7 7.6 - - - +
141S LEU* 1.3 77.8 - - - +
143S ALA* 1.3 56.1 + - - +
145S MET* 3.9 5.2 - - - +
146S LEU* 2.9 33.4 + - - +
174S LEU* 4.1 29.2 - - + +
177S ILE* 5.6 6.1 - - + -
178S GLU* 5.1 3.6 - - + +
453S LEU* 5.8 3.4 - - + -
456S TRP* 5.8 0.9 - - - -
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Residues in contact with ALA 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139S ASP 2.9 18.4 + - - +
140S ILE* 3.9 6.5 - - - +
142S MET* 1.3 76.5 - - - +
144S THR* 1.3 60.5 + - - +
146S LEU* 3.9 6.4 + - - +
147S ASN* 3.4 20.1 - - - +
407S ASN* 4.0 25.2 - - + +
442S ALA* 4.3 15.6 - - + +
444S SER* 5.7 6.7 - - - -
453S LEU* 4.6 13.8 - - + +
456S TRP* 5.4 2.7 - - - +
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Residues in contact with THR 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140S ILE 2.9 18.1 + - - -
141S LEU* 3.8 7.0 - - - -
142S MET 3.3 0.2 - - - -
143S ALA* 1.3 77.9 - - - +
145S MET* 1.3 62.0 + - - +
147S ASN* 4.1 7.3 + - - +
151S VAL* 3.9 13.4 - - - +
407S ASN* 5.1 2.2 - - - +
409S GLY* 3.7 25.9 - - - +
410S SER* 5.6 2.0 - - - -
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Residues in contact with MET 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141S LEU 2.9 17.5 + - - +
142S MET 3.9 1.1 - - - +
144S THR* 1.3 78.3 - - - +
146S LEU* 1.3 56.4 + - - +
147S ASN 3.2 7.0 + - - -
148S GLY 4.2 10.6 + - - +
151S VAL* 4.3 18.6 - - - +
152S MET* 4.1 21.8 - - + -
178S GLU* 3.7 32.8 - - + +
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Residues in contact with LEU 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142S MET 2.9 17.4 + - - +
143S ALA 4.0 4.0 - - - +
145S MET* 1.3 74.1 - - - +
147S ASN* 1.3 58.1 + - - +
148S GLY 3.8 1.3 - - - +
177S ILE* 3.8 24.5 - - + +
178S GLU* 4.7 3.1 - - - +
440S LYS* 4.8 4.5 - - - +
442S ALA* 4.7 2.1 + - - +
456S TRP* 3.4 40.4 - - + +
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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