Contacts of the helix formed by residues 126 - 137 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K GLU* 5.6 1.2 + - - -
107K ARG 4.3 0.7 - - - -
109K GLY* 4.3 6.6 + - - -
110K PHE* 3.8 9.2 - - - -
124K GLY* 3.4 2.4 - - - -
125K ILE* 1.3 78.2 - - - +
127K GLY* 1.3 65.4 + - - +
128K PRO* 3.4 5.5 - - - +
129K GLU* 3.0 30.5 + - - +
130K TYR* 2.8 23.9 + - - +
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K ALA* 3.6 14.9 + - - -
107K ARG* 3.4 32.0 + - - -
125K ILE* 3.6 1.4 - - - +
126K GLY* 1.3 75.9 - - - +
128K PRO* 1.3 68.7 - - - +
130K TYR* 3.1 5.2 + - - +
131K ILE* 2.8 29.3 + - - +
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Residues in contact with PRO 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 3.6 24.7 - - + -
13K PHE* 4.1 21.8 - - + -
14K GLU* 4.7 1.3 - - - +
104K ALA* 3.9 12.9 - - + +
126K GLY* 3.5 2.2 - - - +
127K GLY* 1.3 88.4 - - - +
129K GLU* 1.3 69.7 + - - +
131K ILE* 3.0 14.5 + - + +
132K TYR* 2.7 34.5 + - - +
212K SER* 3.6 9.8 + - - -
216K MET* 4.4 22.0 - - + -
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Residues in contact with GLU 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 4.8 8.5 - - + -
7K GLU 3.5 22.4 - - - +
8K ASP* 4.5 4.0 - - - -
9K VAL* 3.9 19.1 - - - +
11K PHE* 3.7 9.3 - - + -
14K GLU* 3.3 20.5 - - - +
110K PHE* 3.0 29.1 - - + -
123K ASN 4.2 0.9 - - - +
126K GLY* 3.0 14.9 + - - +
127K GLY 3.2 0.2 - - - -
128K PRO* 1.3 105.6 - - - +
130K TYR* 1.3 55.2 + - - +
132K TYR* 2.8 11.6 + - - +
133K SER* 2.7 38.4 + - - -
257K SR 4.0 7.0 - - - -
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Residues in contact with TYR 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 4.2 23.5 - - + +
107K ARG* 3.6 41.7 - - + -
108K ALA 5.4 4.5 - - - -
109K GLY* 5.1 5.4 - - - -
126K GLY 2.8 13.5 + - - +
127K GLY* 3.1 11.2 + - - +
129K GLU* 1.3 75.2 - - - +
131K ILE* 1.3 71.5 + - + +
133K SER* 3.1 6.8 + - - -
134K VAL* 2.8 50.3 + - + +
159K ALA* 4.0 19.3 - - + -
160K PHE* 3.4 22.5 - - - -
161K GLN* 4.9 3.3 + - + -
162K ASN* 5.1 2.9 + - - -
301K HEM 3.2 27.8 + - + +
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Residues in contact with ILE 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K MET* 3.6 28.3 - - + -
104K ALA* 3.7 27.1 - - + +
107K ARG* 5.6 0.7 - - + -
127K GLY 2.8 17.9 + - - +
128K PRO* 3.2 9.2 - - + +
130K TYR* 1.3 82.8 - - + +
132K TYR* 1.3 67.4 + - - +
134K VAL* 3.0 8.0 + - - +
135K LEU* 3.0 31.7 + - + +
212K SER* 3.8 12.6 - - - +
215K LEU* 4.4 26.2 - - + -
301K HEM 3.9 22.0 - - + -
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Residues in contact with TYR 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K GLU* 3.9 23.6 - - + -
9K VAL* 3.3 31.8 - - + +
11K PHE* 4.6 3.1 - + + -
128K PRO 2.7 16.1 + - - +
129K GLU* 2.8 14.8 + - - +
131K ILE* 1.3 71.2 - - - +
133K SER* 1.3 76.8 + - - +
135K LEU* 2.9 11.2 + - - +
136K THR* 2.9 45.3 + - + +
205K HIS* 3.2 50.4 + + - +
208K ALA* 3.8 4.0 - - + -
209K GLU* 3.6 29.8 - - + -
212K SER* 3.5 10.0 + - - +
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Residues in contact with SER 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 3.5 10.0 - - - +
7K GLU* 3.1 35.8 + - - +
129K GLU 2.7 18.1 + - - -
130K TYR* 3.3 10.1 - - - -
132K TYR* 1.3 78.4 - - - +
134K VAL* 1.3 54.4 + - - +
136K THR* 3.0 5.1 + - - -
137K GLY* 2.5 37.4 + - - -
159K ALA* 3.8 18.8 - - - -
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Residues in contact with VAL 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K TYR* 2.8 65.1 + - + +
131K ILE* 3.4 7.9 - - - +
133K SER* 1.3 72.8 - - - +
135K LEU* 1.3 62.7 + - + +
137K GLY 3.5 1.9 + - - -
138K PHE* 3.4 6.2 - - - -
157K ASN* 2.9 42.9 + - - +
159K ALA* 4.2 5.2 - - + -
160K PHE* 4.9 1.6 - - + +
183K ILE* 4.2 20.9 - - + -
185K MET* 4.3 15.0 - - + -
301K HEM 5.1 10.3 - - + -
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Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K ILE* 3.0 19.9 + - + +
132K TYR 2.9 6.7 + - - +
134K VAL* 1.3 77.7 - - + +
136K THR* 1.3 62.6 + - - +
138K PHE* 3.6 16.6 - - - +
185K MET* 4.2 6.7 - - + -
188K PRO* 3.6 25.8 - - + +
189K LEU* 4.2 11.4 - - + +
204K VAL* 4.8 7.5 - - - +
208K ALA* 3.9 22.7 - - + +
211K VAL* 3.6 19.7 - - + -
212K SER* 4.5 1.1 - - - +
301K HEM 3.5 53.2 - - + -
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Residues in contact with THR 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K GLU* 5.1 9.2 - - + -
132K TYR* 2.9 44.4 + - + +
133K SER* 3.4 10.5 - - - -
135K LEU* 1.3 79.6 - - - +
137K GLY* 1.3 56.6 + - - +
138K PHE* 2.9 14.9 + - - +
204K VAL* 5.4 7.8 - - - +
205K HIS* 5.5 3.5 - - - -
208K ALA* 4.4 4.0 - - - +
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Residues in contact with GLY 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K SER 2.5 21.3 + - - -
134K VAL 3.9 2.5 - - - -
135K LEU 3.4 1.4 - - - -
136K THR* 1.3 69.2 - - - +
138K PHE* 1.3 57.0 + - - +
139K PRO* 3.0 8.3 - - - +
157K ASN* 3.2 14.1 - - - -
158K ARG* 2.8 43.0 + - - +
159K ALA* 4.8 1.1 - - - -
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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