Contacts of the helix formed by residues 126 - 137 (chain H) in PDB entry 2QJK
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 126 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14H GLU* 5.7 1.0 + - - -
109H GLY* 4.0 6.4 + - - -
110H PHE* 3.6 12.1 - - - -
124H GLY* 3.2 3.8 - - - -
125H ILE* 1.3 79.4 - - - +
127H GLY* 1.3 64.8 + - - +
128H PRO* 4.3 1.4 - - - +
129H GLU* 3.2 32.7 + - - +
130H TYR* 2.9 22.9 + - - +
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ALA* 3.3 16.2 + - - -
107H ARG* 3.2 27.4 + - - -
125H ILE* 3.4 5.5 - - - +
126H GLY* 1.3 74.8 - - - +
128H PRO* 1.3 69.4 - - - +
130H TYR* 3.1 5.1 + - - +
131H ILE* 2.9 27.9 + - - +
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Residues in contact with PRO 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H PHE* 3.6 26.5 - - + -
13H PHE* 4.1 21.8 - - + -
14H GLU* 5.2 1.8 - - - +
104H ALA* 3.9 10.2 - - + +
126H GLY* 4.3 0.9 - - - +
127H GLY* 1.3 87.6 - - - +
129H GLU* 1.3 70.2 + - - +
131H ILE* 3.1 14.8 + - + +
132H TYR* 2.7 34.1 + - - +
212H SER* 3.6 10.4 + - - -
216H MET* 4.4 24.0 - - + -
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.9 4.5 - - + -
7H GLU 3.6 20.2 - - - +
9H VAL* 4.0 19.3 - - - +
11H PHE* 3.8 6.5 - - + -
14H GLU* 3.3 27.7 - - - +
110H PHE* 2.9 32.0 - - + -
123H ASN 3.9 1.0 - - - +
126H GLY* 3.2 19.9 - - - +
128H PRO* 1.3 105.7 - - - +
130H TYR* 1.3 56.8 + - - +
132H TYR* 2.8 10.5 + - - +
133H SER* 2.6 39.4 + - - -
257H SR 3.4 2.8 - - - -
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Residues in contact with TYR 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.2 23.2 - - + +
107H ARG* 3.5 35.0 - - + -
108H ALA 4.4 13.0 - - - +
109H GLY* 4.5 0.2 - - - -
126H GLY 2.9 13.1 + - - +
127H GLY* 3.3 9.6 - - - +
129H GLU* 1.3 75.9 - - - +
131H ILE* 1.3 70.4 + - + +
133H SER* 3.1 6.4 + - - -
134H VAL* 2.8 46.6 + - + +
159H ALA* 3.9 20.4 - - + -
160H PHE* 3.4 17.8 - - - -
161H GLN* 4.9 2.8 + - + -
162H ASN* 5.1 2.8 + - - -
301H HEM 2.5 41.6 + - + +
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Residues in contact with ILE 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H MET* 3.6 33.4 - - + +
104H ALA* 3.7 26.5 - - + +
107H ARG* 5.5 0.2 - - + -
127H GLY 2.9 18.0 + - - +
128H PRO* 3.3 9.2 - - + +
130H TYR* 1.3 83.1 - - + +
132H TYR* 1.3 68.5 + - - +
134H VAL* 3.1 6.4 + - - +
135H LEU* 3.0 31.2 + - + +
212H SER* 3.8 12.8 - - - +
215H LEU* 4.4 26.9 - - + -
301H HEM 4.0 17.9 - - + -
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Residues in contact with TYR 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU* 4.0 17.9 - - + -
9H VAL* 3.3 31.9 - - + -
11H PHE* 4.6 2.7 - + + -
128H PRO 2.7 15.7 + - - +
129H GLU* 2.8 13.6 + - - +
131H ILE* 1.3 71.1 - - - +
133H SER* 1.3 79.7 + - - +
135H LEU* 2.9 10.8 + - - +
136H THR* 2.9 47.2 + - + +
205H HIS* 3.1 51.7 + + - +
208H ALA* 3.8 3.8 - - + -
209H GLU* 3.5 31.0 - - + -
212H SER* 3.5 10.9 + - - +
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Residues in contact with SER 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 3.6 8.6 - - - -
7H GLU* 3.1 36.8 + - - +
129H GLU 2.6 19.2 + - - -
130H TYR* 3.3 10.1 - - - -
132H TYR* 1.3 78.6 - - - +
134H VAL* 1.3 54.8 + - - +
136H THR* 3.0 4.7 + - - -
137H GLY* 2.4 37.9 + - - -
159H ALA* 3.8 18.8 - - - +
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Residues in contact with VAL 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H TYR* 2.8 64.4 + - + +
131H ILE* 3.5 7.0 - - - +
133H SER* 1.3 72.3 - - - +
135H LEU* 1.3 64.3 + - + +
137H GLY 3.4 2.3 + - - -
138H PHE* 3.6 4.9 - - - -
157H ASN* 2.9 44.1 + - - +
159H ALA* 4.2 4.9 - - + -
160H PHE* 4.9 2.0 - - + +
183H ILE* 4.3 18.4 - - + -
185H MET* 4.3 15.5 - - + -
301H HEM 4.8 11.7 - - + -
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Residues in contact with LEU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H ILE* 3.0 20.2 + - + +
132H TYR 2.9 6.8 + - - +
134H VAL* 1.3 78.3 - - + +
136H THR* 1.3 62.4 + - - +
137H GLY 3.6 0.2 + - - -
138H PHE* 3.8 15.8 + - - +
185H MET* 4.2 6.5 - - + -
188H PRO* 3.6 29.6 - - + +
189H LEU* 4.3 8.5 + - + +
204H VAL* 4.9 8.4 - - - +
208H ALA* 3.9 24.0 - - + +
211H VAL* 3.6 21.5 - - + -
212H SER* 4.5 1.1 - - - +
301H HEM 3.6 47.8 - - + -
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Residues in contact with THR 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU* 5.3 8.3 - - + -
132H TYR* 2.9 43.6 + - + +
133H SER* 3.4 10.5 - - - -
135H LEU* 1.3 77.2 - - - +
137H GLY* 1.3 57.5 + - - +
138H PHE* 2.9 15.7 + - - +
204H VAL* 5.4 8.4 + - - +
205H HIS* 5.5 3.7 - - - -
208H ALA* 4.4 3.9 - - - +
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Residues in contact with GLY 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H SER 2.4 22.1 + - - -
134H VAL 3.8 2.9 - - - -
135H LEU 3.3 1.0 - - - -
136H THR* 1.3 68.7 - - - +
138H PHE* 1.3 59.0 + - - +
139H PRO* 3.0 8.0 - - - +
157H ASN* 3.2 12.7 - - - -
158H ARG* 2.8 41.8 + - - +
159H ALA* 4.8 1.3 - - - -
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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