Contacts of the helix formed by residues 135 - 145 (chain A) in PDB entry 2OQ4
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PRO 4.7 2.0 - - - +
133A ASN* 3.3 14.2 + - - +
134A LEU* 1.3 77.8 - - - +
136A PRO* 1.3 74.0 - - + +
137A GLU* 3.6 13.3 + - - +
138A VAL* 3.0 30.4 + - + +
139A VAL* 2.9 22.7 + - - +
202A LEU* 3.7 3.4 - - - -
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Residues in contact with PRO 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 LEU 4.6 0.2 - - - +
135A THR* 1.3 88.9 - - - +
137A GLU* 1.3 64.8 + - - +
139A VAL* 3.4 3.8 - - + +
140A LYS* 2.5 39.0 + - - +
195A ASP* 5.6 0.4 - - - +
198A ALA* 4.1 11.0 - - + +
199A HIS* 3.5 46.9 - - + +
202A LEU* 3.6 20.8 - - + -
206A ARG* 6.0 1.8 - - - +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR* 3.1 11.3 + - - +
136A PRO* 1.3 95.5 - - - +
138A VAL* 1.3 59.1 + - + +
140A LYS* 3.1 33.7 + - - +
141A GLU* 2.8 36.0 + - + +
195A ASP* 4.3 10.4 - - - +
199A HIS* 4.9 3.3 + - - -
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Residues in contact with VAL 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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127A PRO* 5.8 3.1 - - + -
133A ASN 4.7 5.4 - - - +
134A LEU* 4.3 14.4 - - + -
135A THR* 3.0 32.7 + - + +
137A GLU* 1.3 75.0 - - + +
139A VAL* 1.3 59.2 + - - +
141A GLU* 2.8 39.6 + - + +
142A ARG* 2.9 15.9 + - + +
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Residues in contact with VAL 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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134A LEU* 3.5 31.9 - - + -
135A THR 2.9 14.6 + - - +
136A PRO* 3.5 8.3 - - + +
138A VAL* 1.3 75.3 - - - +
140A LYS* 1.3 61.3 + - - +
142A ARG* 3.4 10.7 + - - +
143A LEU* 3.0 23.8 + - - +
162A PHE* 4.9 3.7 - - + -
163A LEU* 4.3 20.6 - - + -
198A ALA* 4.5 9.0 - - - +
201A LEU* 4.3 25.8 - - + -
202A LEU* 3.5 17.7 - - + -
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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 PRO 2.5 21.8 + - - +
137A GLU* 3.1 38.7 + - - +
139A VAL* 1.3 75.1 - - - +
141A GLU* 1.3 62.6 + - - +
143A LEU* 3.4 16.8 + - - +
144A LEU* 3.4 19.0 + - + +
194A LEU* 3.8 27.5 - - + +
195A ASP* 4.3 21.2 + - + +
198A ALA* 4.4 12.3 - - + +
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Residues in contact with GLU 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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137A GLU* 2.8 24.1 + - + +
138A VAL* 2.8 30.9 + - + +
140A LYS* 1.3 75.7 - - - +
142A ARG* 1.3 56.7 + - - +
144A LEU* 3.1 8.9 + - - +
145A SER* 2.7 36.5 + - - -
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Residues in contact with ARG 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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126A GLY* 3.5 4.4 - - - -
127A PRO* 3.2 36.5 - - - +
134A LEU* 6.2 0.7 - - - -
138A VAL* 2.9 14.0 + - + +
139A VAL* 3.5 11.9 - - - +
141A GLU* 1.3 77.3 - - - +
143A LEU* 1.3 61.5 + - - +
145A SER* 2.8 26.4 + - - +
147A ARG* 4.0 14.1 - - - +
148A PHE* 3.2 36.1 - - + +
161A ALA 3.1 23.8 + - - -
162A PHE* 2.7 33.1 + - + -
163A LEU* 4.4 7.0 - - - -
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Residues in contact with LEU 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 VAL 3.0 15.0 + - - +
140A LYS* 3.5 12.3 - - - +
141A GLU 3.2 0.4 - - - -
142A ARG* 1.3 77.5 - - - +
144A LEU* 1.3 60.5 + - - +
148A PHE* 3.9 2.9 - - - -
149A ARG 3.5 13.0 + - - -
153A PHE* 4.0 17.0 - - + -
156A LEU* 4.0 11.0 - - + -
157A LEU* 5.6 0.4 - - + -
162A PHE* 3.8 28.0 - - + -
186A ALA* 2.9 24.1 - - + +
194A LEU* 3.4 29.4 - - + +
197A LEU* 3.2 36.1 - - + -
198A ALA* 4.7 2.7 - - - +
201A LEU* 4.2 10.5 - - + -
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Residues in contact with LEU 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* 3.4 12.5 + - + +
141A GLU* 3.1 8.8 + - - +
143A LEU* 1.3 73.4 - - - +
145A SER* 1.3 70.7 + - - +
146A PRO* 3.5 1.4 - - - +
149A ARG* 3.4 13.7 - - + +
186A ALA 4.1 20.9 - - - +
187A LYS* 5.0 4.7 - - - +
194A LEU* 3.4 35.2 - - + -
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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 GLU 2.7 18.2 + - - -
142A ARG* 2.8 23.4 + - - +
143A LEU 4.1 0.2 - - - +
144A LEU* 1.3 81.2 - - - +
146A PRO* 1.3 71.4 - - - +
147A ARG* 3.6 11.9 + - - +
148A PHE* 3.6 11.4 - - - -
149A ARG* 3.0 20.4 + - - +
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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