Contacts of the helix formed by residues 134 - 145 (chain A) in PDB entry 6O0Z
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR* 5.1 3.9 + - - -
132A TYR* 3.9 18.4 - - - +
133A PRO* 1.3 85.3 - - + +
135A ILE* 1.3 64.2 + - - +
136A TYR* 3.5 18.1 + - - +
137A HIS* 2.7 29.8 + - - -
138A LEU* 4.0 2.4 + - - +
325A TYR* 4.5 17.0 - - + +
402A GLN* 5.0 6.5 - - + +
44B U 3.9 13.7 - - + +
45B U 3.7 33.9 - - - +
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Residues in contact with ILE 135 (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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128A TYR* 4.4 11.2 - - - +
134A THR* 1.3 74.9 - - - +
136A TYR* 1.3 77.1 + - + +
137A HIS 3.4 0.4 - - - -
138A LEU* 3.3 29.5 + - + +
139A ARG* 2.9 32.8 + - + +
156A LEU* 4.5 22.0 - - + +
157A ALA* 5.1 1.6 - - - +
160A HIS* 3.8 48.5 - - + +
45B U 3.5 6.3 + - - +
46B A 4.2 24.2 - - - +
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Residues in contact with TYR 136 (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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134A THR* 3.3 16.3 - - - +
135A ILE* 1.3 87.4 - - + +
137A HIS* 1.3 59.6 + - - +
139A ARG* 3.8 29.3 + - - +
140A LYS* 2.9 30.5 + - - +
160A HIS* 4.1 13.8 - + - -
317A LEU* 5.1 9.0 - - + -
318A SER* 3.7 24.1 - - - +
321A MET* 3.8 48.4 - - + +
322A ILE* 4.5 5.4 - - + -
402A GLN* 4.5 18.1 + - + -
403A ARG* 3.9 22.8 + - + -
407A ASN* 5.2 2.8 + - - -
415A HIS* 6.4 0.2 - + - -
45B U 5.1 3.1 - - - -
46B A 5.1 1.8 - - - -
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Residues in contact with HIS 137 (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 LYS 5.2 1.1 - - - +
132A TYR* 4.0 12.6 - - + -
133A PRO* 3.6 35.4 - - + +
134A THR* 2.7 30.7 + - - +
135A ILE 3.4 0.4 - - - -
136A TYR* 1.3 76.2 - - - +
138A LEU* 1.3 56.5 + - - +
140A LYS* 3.5 1.6 + - - +
141A LYS* 2.9 30.0 + - - +
322A ILE* 3.6 40.1 - - + +
325A TYR* 3.8 35.8 - + + -
326A ASP* 5.8 0.4 + - - -
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Residues in contact with LEU 138 (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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128A TYR* 4.3 12.6 - - + +
132A TYR* 3.8 29.5 - - + +
134A THR 4.0 5.7 + - - +
135A ILE* 3.3 33.4 + - + +
136A TYR 3.2 0.6 - - - -
137A HIS* 1.3 79.4 - - - +
139A ARG* 1.3 57.9 + - - +
141A LYS* 3.4 2.7 + - + -
142A LEU* 2.9 46.8 + - + +
153A LEU* 3.8 52.5 - - + +
156A LEU* 4.8 5.2 - - + -
157A ALA* 4.8 4.5 - - + -
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Residues in contact with ARG 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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135A ILE* 2.9 25.5 + - + +
136A TYR* 3.8 20.5 + - - +
137A HIS 3.3 0.2 - - - -
138A LEU* 1.3 78.3 - - - +
140A LYS* 1.3 56.1 + - - +
142A LEU* 3.3 6.2 + - - +
143A VAL* 2.9 34.5 + - + +
157A ALA* 4.3 18.6 - - + -
160A HIS* 3.2 37.4 + - - -
161A MET* 3.5 34.7 - - + +
317A LEU* 4.4 7.1 - - - +
318A SER* 3.9 11.1 + - - +
415A HIS* 3.6 28.9 + - - -
418A GLU* 2.5 36.9 + - - +
422A ILE* 4.6 2.4 - - + +
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Residues in contact with LYS 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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136A TYR 2.9 17.2 + - - +
137A HIS 4.0 2.9 - - - +
139A ARG* 1.3 76.9 - - - +
141A LYS* 1.3 59.1 + - - +
143A VAL* 3.9 4.0 - - - -
144A ASP* 2.9 49.6 + - - +
313A THR* 4.9 10.3 - - - +
315A ALA* 5.2 4.5 - - + +
318A SER* 3.8 10.7 - - - -
319A ALA* 4.2 29.2 - - + +
322A ILE* 3.7 28.1 - - + +
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Residues in contact with LYS 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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132A TYR* 3.3 34.0 + - + +
137A HIS 2.9 18.7 + - - +
138A LEU* 3.8 5.8 - - + +
140A LYS* 1.3 77.7 - - - +
142A LEU* 1.3 63.5 + - + +
144A ASP* 5.0 1.3 - - - -
145A SER* 2.3 61.5 + - - +
147A ASP* 5.3 14.7 + - - +
149A ALA* 4.3 23.0 - - - +
153A LEU* 5.5 3.8 - - - +
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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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138A LEU* 2.9 31.1 + - + +
139A ARG 3.3 3.8 + - - +
141A LYS* 1.3 82.4 - - + +
143A VAL* 1.3 65.4 + - - +
145A SER* 3.9 9.7 - - - +
149A ALA* 3.8 29.2 - - + -
153A LEU* 3.9 15.0 - - + +
154A ILE* 4.2 15.9 - - + -
157A ALA* 3.8 28.7 - - + -
422A ILE* 4.2 22.7 - - + +
425A ARG* 4.3 11.6 - - - +
426A GLN* 4.3 17.5 - - + +
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Residues in contact with VAL 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 ARG 2.9 20.5 + - - +
140A LYS 3.9 3.1 - - - +
142A LEU* 1.3 80.0 - - - +
144A ASP* 1.3 74.2 + - - +
145A SER 4.3 0.2 - - - +
314A LYS* 4.2 17.9 - - + -
315A ALA* 4.1 27.1 - - + -
418A GLU* 4.0 17.5 - - + +
421A ALA* 4.3 17.0 - - + +
422A ILE* 3.7 24.5 - - + +
425A ARG* 3.2 25.3 + - - +
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Residues in contact with ASP 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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140A LYS* 2.9 38.8 + - + +
141A LYS* 5.0 1.3 - - - -
143A VAL* 1.3 91.3 - - - +
145A SER* 1.3 62.8 + - - +
146A THR* 3.7 4.5 - - - +
312A ILE 5.3 1.1 - - - +
313A THR* 3.4 28.2 + - - -
314A LYS* 4.2 4.0 + - - +
315A ALA* 5.3 0.2 - - - +
425A ARG* 2.9 20.6 + - - +
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Residues in contact with SER 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 LYS* 2.3 54.8 + - - +
142A LEU* 3.9 8.5 - - - +
144A ASP* 1.3 80.9 - - - +
146A THR* 1.3 60.1 + - - +
147A ASP* 3.5 14.6 + - - +
425A ARG* 3.6 14.4 - - - +
426A GLN* 4.6 4.0 - - - +
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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