Contacts of the helix formed by residues 151 - 166 (chain B) in PDB entry 3K9L
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 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ILE* 4.1 2.4 - - - +
143B GLU 3.9 13.7 - - - -
144B THR* 3.4 12.4 - - - +
149B ARG 3.2 1.8 + - - -
150B GLN* 1.3 76.2 - - - +
152B VAL* 1.3 58.1 + - - +
153B GLU 3.6 1.3 - - - -
154B ASP* 3.3 17.6 - - - +
155B ALA* 2.8 25.1 + - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.8 42.0 - - + +
22B GLN* 4.2 6.3 - - + -
23B LEU* 4.1 17.3 - - + +
144B THR* 4.4 5.6 - - - -
145B SER 3.5 20.9 - - - +
146B ALA* 4.2 4.0 - - - -
149B ARG* 3.3 26.3 + - + +
150B GLN 3.1 3.1 - - - +
151B GLY* 1.3 73.9 - - - +
153B GLU* 1.3 69.4 + - + +
155B ALA* 3.0 12.7 + - - +
156B PHE* 3.2 27.3 + - + -
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 5.6 0.2 - - - -
23B LEU* 4.1 23.6 - - + -
149B ARG* 2.7 36.1 + - - +
152B VAL* 1.3 79.1 - - + +
154B ASP* 1.3 58.5 + - - +
156B PHE 3.3 0.5 + - - -
157B TYR* 2.9 63.3 + - + +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASP* 3.8 32.6 - - - +
157A TYR* 4.9 7.6 - - - +
158A THR* 5.3 0.7 + - - -
161A ARG* 3.0 36.1 + - - -
142B ILE* 4.2 4.5 - - + +
151B GLY* 3.3 20.8 - - - +
152B VAL 3.1 0.2 - - - -
153B GLU* 1.3 78.5 - - - +
155B ALA* 1.3 61.3 + - - +
157B TYR* 4.2 0.4 - - - +
158B THR* 2.8 43.4 + - - -
161B ARG* 5.0 0.5 + - - -
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 6.4 0.4 - - + -
79B LEU* 3.8 13.6 - - + +
112B VAL* 4.3 2.3 - - - +
114B VAL* 4.1 21.5 - - + -
142B ILE* 3.8 15.5 - - + +
144B THR* 3.9 16.4 - - + -
151B GLY 2.8 19.8 + - - +
152B VAL* 3.0 4.7 + - - +
154B ASP* 1.3 74.9 - - - +
156B PHE* 1.3 63.6 + - + +
158B THR* 3.8 2.3 - - - -
159B LEU* 3.2 22.0 + - - +
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 25.3 - - + +
8B VAL* 4.1 20.4 - - + -
19B LEU* 3.7 32.5 - - + -
20B THR* 4.2 9.4 - - - -
23B LEU* 3.3 43.7 - - + -
53B LEU* 5.6 1.3 - - + -
55B ILE* 4.1 10.8 - - + -
79B LEU* 3.5 29.2 - - + -
152B VAL* 3.2 26.3 + - + +
153B GLU 4.0 2.7 - - - +
155B ALA* 1.3 79.8 - - + +
157B TYR* 1.3 62.8 + - + +
159B LEU* 3.3 6.5 + - + +
160B VAL* 3.0 30.0 + - - +
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Residues in contact with TYR 157 (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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154A ASP* 4.5 6.3 - - - +
23B LEU* 4.6 14.0 - - + +
44B VAL* 4.8 10.1 - - + +
45B VAL 4.3 11.4 + - - -
46B ILE* 3.8 44.4 - - + +
47B ASP 5.8 0.4 - - - -
53B LEU* 4.9 7.4 - - + -
153B GLU* 2.9 48.5 + - + +
154B ASP 4.2 0.7 - - - +
156B PHE* 1.3 76.6 - - + +
158B THR* 1.3 62.4 + - - +
159B LEU 3.1 1.1 - - - -
160B VAL* 3.1 8.5 + - - +
161B ARG* 2.8 58.0 + - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 4.7 10.0 + - + +
161A ARG* 4.1 5.3 + - - +
112B VAL* 4.0 5.8 - - + -
140B PRO* 4.0 26.7 - - + -
142B ILE* 3.4 21.3 - - + +
154B ASP* 2.8 34.6 + - - -
155B ALA 3.8 1.6 - - - -
157B TYR* 1.3 77.9 - - - +
159B LEU* 1.3 56.9 + - - +
161B ARG* 3.1 17.5 + - + +
162B GLU* 2.8 30.8 + - + +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.1 24.9 - - + -
77B GLY* 3.7 14.4 - - - +
78B PHE 3.6 37.0 - - - +
79B LEU* 3.6 22.2 - - + +
110B PRO* 3.9 5.6 - - + +
111B MET 3.8 20.4 - - - +
112B VAL* 3.8 14.6 - - + -
155B ALA 3.2 12.0 + - - +
156B PHE* 3.6 9.4 - - + +
157B TYR 3.1 0.8 - - - -
158B THR* 1.3 77.9 - - - +
160B VAL* 1.3 66.0 + - - +
162B GLU* 3.1 2.5 + - + +
163B ILE* 3.0 27.1 + - - +
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Residues in contact with VAL 160 (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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4B TYR* 3.9 22.0 - - + -
6B LEU* 4.3 8.3 - - + -
46B ILE* 4.0 15.9 - - + -
53B LEU* 3.7 30.5 - - + -
156B PHE 3.0 15.4 + - - +
157B TYR* 3.1 9.2 + - - +
159B LEU* 1.3 74.8 - - - +
161B ARG* 1.3 64.2 + - - +
163B ILE* 3.1 12.3 + - - +
164B ARG* 3.0 53.5 + - - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 5.0 9.3 - - + +
141A TYR 3.8 8.7 - - - +
142A ILE* 3.7 36.8 - - - +
151A GLY* 5.8 1.4 - - - -
154A ASP* 3.1 32.9 + - - +
158A THR* 4.7 3.1 + - - -
46B ILE* 4.7 1.4 - - + +
47B ASP* 2.7 41.6 + - - +
154B ASP* 5.0 0.6 + - - -
157B TYR* 2.8 45.7 + - - +
158B THR* 3.1 21.6 + - + +
160B VAL* 1.3 72.7 - - + +
162B GLU* 1.3 63.7 + - + +
164B ARG* 3.2 25.8 + - - +
165B GLN* 3.3 24.8 + - - +
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Residues in contact with GLU 162 (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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140A PRO* 5.4 0.9 - - - +
162A GLU* 4.4 10.2 - - - +
165A GLN* 5.3 3.4 + - - +
110B PRO* 4.2 10.8 - - + -
111B MET 4.5 8.6 + - - +
112B VAL* 4.5 0.4 - - + -
139B ILE* 5.5 1.7 - - - +
140B PRO* 3.9 36.1 - - + +
158B THR* 2.8 23.2 + - + +
159B LEU* 3.1 12.5 + - + +
161B ARG* 1.3 76.7 - - + +
163B ILE* 1.3 60.3 + - - +
165B GLN* 3.3 23.6 + - - +
166B HIS* 2.6 54.5 + - - +
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Residues in contact with ILE 163 (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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4B TYR* 4.0 23.1 - - + -
6B LEU* 3.4 33.7 - - + -
76B GLU* 3.9 29.8 - - + +
77B GLY* 3.8 15.9 - - - +
110B PRO* 3.7 24.9 - - + +
159B LEU 3.0 17.4 + - - +
160B VAL* 3.4 9.9 - - - +
162B GLU* 1.3 77.0 - - - +
164B ARG* 1.3 62.3 + - - +
166B HIS* 3.3 19.8 + - - +
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Residues in contact with ARG 164 (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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131A GLN* 3.4 37.1 + - + +
135A ARG* 3.0 32.3 + - - +
141A TYR* 4.6 2.8 + - - -
4B TYR* 2.9 29.3 + - + +
46B ILE* 3.0 36.0 + - - +
47B ASP* 3.1 33.7 + - - +
49B GLU* 3.2 16.2 + - - +
51B CYS* 4.7 0.8 - - - -
160B VAL* 3.0 28.5 + - - +
161B ARG* 3.2 19.7 + - - +
163B ILE* 1.3 77.2 - - - +
165B GLN* 1.3 60.3 + - + +
166B HIS 3.5 2.1 + - - +
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Residues in contact with GLN 165 (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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135A ARG* 3.5 25.5 - - + +
138A GLY* 3.5 18.5 + - - -
139A ILE* 3.4 31.0 - - - +
140A PRO* 3.6 30.1 - - + +
162A GLU* 5.3 3.4 + - - -
161B ARG* 3.3 16.7 + - - +
162B GLU* 3.6 21.2 + - - +
163B ILE 3.2 1.0 - - - -
164B ARG* 1.3 78.5 - - + +
166B HIS* 1.3 80.9 + - + +
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Residues in contact with HIS 166 (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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135A ARG* 5.0 5.5 + - - -
108B ASP* 4.3 29.6 + - - +
110B PRO* 3.4 36.4 - - + +
162B GLU* 2.6 48.9 + - - +
163B ILE 3.3 14.6 + - - +
164B ARG 4.2 3.1 - - - +
165B GLN* 1.3 100.2 + - + +
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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