Contacts of the helix formed by residues 141 - 153 (chain B) in PDB entry 3KAS
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 SER 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLY 5.8 0.7 - - - -
106B ASN* 3.3 27.9 + - - -
108B PHE* 4.0 8.6 - - - -
136B LEU* 3.4 20.9 - - - +
138B LYS* 2.9 19.9 + - - +
140B ASP* 1.3 78.0 + - - +
142B SER* 1.3 60.2 + - - +
143B TRP* 2.9 9.2 + - - +
144B ALA* 3.4 16.8 + - - +
145B ILE 4.1 1.0 + - - -
219B GLN* 4.0 10.6 + - - -
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO 5.2 1.6 - - - -
132B LEU* 3.0 45.4 + - - +
133B GLY* 3.3 4.0 - - - -
136B LEU* 3.7 12.8 - - - +
139B SER* 2.7 25.2 + - - -
140B ASP 3.1 0.4 - - - -
141B SER* 1.3 78.1 + - - +
143B TRP* 1.3 57.9 + - - +
145B ILE* 3.1 6.3 + - - +
146B HIS* 2.8 30.1 + - - +
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU 5.5 2.4 + - - -
88B LEU* 3.8 31.5 - - + +
89B PRO* 4.3 13.6 - - + +
103B GLY* 5.9 3.8 - - - -
140B ASP 3.6 17.3 + - - +
141B SER* 2.9 2.6 - - - -
142B SER* 1.3 79.3 - - - +
144B ALA* 1.3 71.9 + - + +
146B HIS* 3.0 19.4 + + + +
147B TRP* 2.8 45.4 + + + +
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Residues in contact with ALA 144 (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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89B PRO* 4.1 16.2 - - + -
101B MET* 3.5 17.4 - - - +
103B GLY* 4.2 13.0 - - - +
108B PHE* 3.9 26.7 - - + -
141B SER* 3.4 8.7 + - - +
142B SER 3.3 0.8 - - - -
143B TRP* 1.3 87.4 - - + +
145B ILE* 1.3 56.6 + - - +
147B TRP* 3.5 1.9 + - - +
148B PHE* 2.9 28.4 + - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B MET* 3.9 14.4 - - + -
108B PHE* 3.6 32.1 - - + -
132B LEU* 4.2 16.2 - - + -
136B LEU* 3.9 25.1 - - + -
141B SER 4.2 1.6 - - - +
142B SER* 3.1 6.2 + - - +
144B ALA* 1.3 75.6 - - - +
146B HIS* 1.3 60.4 + - - +
148B PHE* 3.6 3.1 - - + +
149B SER* 2.8 44.0 + - - +
175B ILE* 4.4 25.4 - - + -
217B ILE* 4.2 28.3 - - + -
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 3.4 34.0 - - + +
130B GLU* 5.8 0.2 - - - -
132B LEU* 3.7 11.8 - - + +
142B SER 2.8 13.8 + - - +
143B TRP* 3.0 25.9 + + + +
145B ILE* 1.3 74.8 - - - +
147B TRP* 1.3 65.8 + - - +
149B SER* 3.3 1.0 + - - -
150B ASN* 3.2 33.1 + - - +
156B TRP* 3.6 26.9 + + - -
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Residues in contact with TRP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.2 32.9 - - + +
89B PRO* 3.5 53.2 - - + -
91B LEU* 4.1 25.4 - - + -
101B MET* 3.9 12.1 - - - -
143B TRP* 2.8 33.8 + + + +
144B ALA 3.7 2.0 - - - +
146B HIS* 1.3 74.7 - - - +
148B PHE* 1.3 81.5 + + - +
150B ASN* 3.4 5.7 + - + +
151B ALA* 2.8 45.2 + - + +
199B LEU* 5.2 2.5 - - + -
241B HIS* 6.0 2.2 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.7 3.6 - - + -
101B MET* 3.7 24.5 - - + -
110B ILE* 3.8 25.6 - - + -
144B ALA 2.9 18.9 + - - +
145B ILE* 3.6 4.7 - - - +
147B TRP* 1.3 85.5 - + - +
149B SER* 1.3 67.7 + - - +
151B ALA* 3.2 3.1 + - - +
152B LEU* 2.9 53.4 + - + +
177B PHE* 5.2 1.1 - + - -
196B MET* 4.2 12.3 - - - -
199B LEU* 3.7 25.8 - - + -
200B PHE* 4.3 9.2 - + - -
215B LEU* 4.5 6.1 - - + -
217B ILE* 3.8 31.4 - - + -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 5.6 0.2 - - - +
145B ILE* 2.8 33.0 + - - +
146B HIS 3.7 0.2 - - - -
148B PHE* 1.3 73.3 - - - +
150B ASN* 1.3 61.1 + - - +
152B LEU* 3.2 12.9 + - - +
154B HIS* 2.9 37.8 + - - +
156B TRP* 3.7 31.7 - - - -
162B MET* 4.0 4.6 - - - +
177B PHE* 3.7 22.8 - - - -
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Residues in contact with ASN 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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146B HIS* 3.2 27.4 + - - +
147B TRP* 3.7 8.4 - - + +
149B SER* 1.3 72.4 - - - +
151B ALA* 1.3 60.4 + - - +
152B LEU 2.9 4.7 - - - -
153B GLY* 2.8 21.7 + - - -
154B HIS 3.9 11.0 - - - +
156B TRP* 2.7 33.7 + - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TRP* 2.8 47.5 + - + +
148B PHE* 3.5 7.4 - - - +
150B ASN* 1.3 73.4 - - - +
152B LEU* 1.3 59.2 + - - +
153B GLY* 3.6 0.3 + - - -
195B GLY* 4.7 3.3 - - - -
198B HIS* 5.8 0.7 - - - +
199B LEU* 3.9 30.5 - - + +
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Residues in contact with LEU 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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148B PHE* 2.9 33.9 + - + +
149B SER* 3.2 12.1 - - - +
150B ASN 2.9 0.2 - - - -
151B ALA* 1.3 78.7 - - - +
153B GLY* 1.3 56.5 + - - +
154B HIS 3.6 0.4 - - - -
177B PHE* 4.3 18.4 - - + -
191B LYS 3.7 11.1 - - - +
192B ILE* 3.8 37.1 - - + +
195B GLY* 3.5 18.5 - - - -
196B MET* 3.8 32.8 - - + +
199B LEU* 3.6 25.4 - - + -
215B LEU* 4.0 8.5 - - + -
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Residues in contact with GLY 153 (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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150B ASN 2.8 12.4 + - - -
151B ALA 3.3 0.4 - - - -
152B LEU* 1.3 79.8 - - - +
154B HIS* 1.3 62.2 + - - +
155B ASP* 3.3 1.6 + - - +
191B LYS* 2.6 38.4 + - - -
192B ILE* 4.8 1.6 - - - -
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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