Contacts of the helix formed by residues 142 - 152 (chain B) in PDB entry 1K7E
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 GLN 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B GLY 4.2 2.2 - - - +
112B ALA* 3.3 30.8 + - - +
134B MET* 3.5 15.5 - - + -
138B ASP* 3.0 14.5 + - + +
139B VAL 3.0 7.2 + - - -
141B ARG* 1.3 100.3 + - + +
143B SER* 1.3 58.7 + - - +
144B PRO* 3.4 9.3 - - - +
145B ASN* 3.2 13.7 + - + -
146B VAL* 2.9 26.0 + - - +
302B ALA* 3.8 27.1 - - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL 3.6 3.4 + - - -
140B GLU* 3.9 12.5 + - - -
141B ARG 3.8 1.4 - - - -
142B GLN* 1.3 69.4 - - - +
144B PRO* 1.3 63.3 - - - +
146B VAL* 3.5 8.4 - - - +
147B PHE* 2.7 37.2 + - - +
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Residues in contact with PRO 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG 5.3 0.7 - - - +
142B GLN* 3.4 8.3 - - - +
143B SER* 1.3 93.8 - - - +
145B ASN* 1.3 69.5 + - - +
146B VAL 3.0 0.3 + - - -
147B PHE* 3.1 6.8 + - + +
148B ARG* 2.8 48.3 + - - +
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 2.9 24.9 + - - +
113B GLY* 3.6 22.8 - - - -
114B GLN* 3.9 10.6 + - - +
117B VAL* 3.8 11.2 - - + +
142B GLN* 3.2 17.7 + - + +
144B PRO* 1.3 83.2 - - - +
146B VAL* 1.3 62.3 + - - +
148B ARG* 3.0 31.4 + - - +
149B MET* 2.9 32.4 + - + +
382B LYS* 5.5 11.8 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET* 4.0 21.1 - - - -
139B VAL* 3.9 28.7 - - + +
142B GLN 2.9 24.9 + - - +
143B SER* 2.9 13.4 + - - +
145B ASN* 1.3 72.8 - - - +
147B PHE* 1.3 65.4 + - - +
149B MET* 3.3 10.0 + - + +
150B ARG* 3.2 57.6 + - - +
156B VAL* 4.3 11.3 - - + +
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B SER 2.7 17.2 + - - +
144B PRO* 3.7 5.2 - - + +
146B VAL* 1.3 81.3 - - - +
148B ARG* 1.3 66.4 + - + +
150B ARG* 3.2 11.8 + - + +
151B LEU* 2.8 63.4 + - + +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.2 23.6 - - + -
144B PRO* 2.8 47.2 + - - +
145B ASN* 3.0 34.4 + - - +
147B PHE* 1.3 75.1 - - + +
149B MET* 1.3 63.5 + - - +
151B LEU* 3.3 14.7 + - + +
152B MET* 3.1 29.2 + - - +
382B LYS* 6.0 4.8 - - - +
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 4.3 1.6 - - + -
113B GLY* 3.8 24.7 - - - +
116B GLY* 3.5 7.4 - - - +
117B VAL* 3.5 21.3 - - - +
120B ALA* 4.1 14.8 - - + -
132B ILE* 3.5 29.2 - - + -
134B MET* 4.1 16.8 - - - -
145B ASN* 2.9 38.1 + - + +
146B VAL* 3.9 8.1 - - - +
148B ARG* 1.3 78.4 - - - +
150B ARG* 1.3 63.9 + - - +
152B MET* 3.0 12.0 + - - +
153B GLY 3.4 0.2 + - - -
154B ALA* 3.1 21.2 + - + +
156B VAL* 4.0 22.0 - - + -
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Residues in contact with ARG 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 5.8 2.8 - - - +
146B VAL* 3.2 40.8 + - - +
147B PHE* 3.7 14.4 - - + +
148B ARG 3.1 0.4 - - - -
149B MET* 1.3 77.6 - - - +
151B LEU* 1.4 55.6 + - - +
152B MET 2.9 5.6 - - - -
153B GLY* 2.9 19.6 + - - -
154B ALA 3.5 17.5 + - - +
156B VAL* 3.1 43.9 + - + +
158B PRO* 4.8 9.1 - - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B PHE* 2.8 60.9 + - + +
148B ARG* 3.5 13.7 - - + +
150B ARG* 1.4 71.2 - - - +
152B MET* 1.3 63.7 + - + +
153B GLY 3.2 1.3 + - - -
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Residues in contact with MET 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B HIS* 5.4 6.5 - - + +
117B VAL* 4.2 16.4 - - + +
120B ALA* 4.1 16.3 - - + +
121B LEU* 3.5 43.3 - - + -
123B SER* 5.9 0.3 - - - -
124B ALA* 3.6 25.8 + - + +
148B ARG* 3.1 20.9 + - + +
149B MET 3.0 9.3 + - - +
150B ARG 2.9 2.0 - - - -
151B LEU* 1.3 83.1 - - + +
153B GLY* 1.4 59.0 + - - +
154B ALA 3.3 2.4 + - - -
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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