Contacts of the helix formed by residues 123 - 135 (chain B) in PDB entry 3KQQ
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 TRP 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.7 11.4 - - + -
40B TYR* 4.0 20.6 - + - -
82B PRO 3.5 11.5 + - - -
83B THR* 3.3 41.1 - - + -
84B VAL* 3.6 29.1 - - + +
85B TYR* 4.0 21.5 - - + -
88B LEU* 6.0 0.7 - - + -
110B LEU* 6.1 0.2 - - - +
113B TRP* 3.5 29.7 - + + +
121B PHE* 3.3 51.3 + + - +
122B ASN* 1.3 73.1 + - - +
124B SER* 1.3 57.0 + - - +
125B MET 3.3 2.9 - - - -
126B TYR* 2.8 49.2 + + + +
127B SER* 2.9 13.2 + - - +
144B GLU* 3.8 6.5 + - - +
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Residues in contact with SER 124 (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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122B ASN* 3.0 27.3 + - - -
123B TRP* 1.3 77.3 - - - +
125B MET* 1.3 64.9 + - - +
127B SER* 3.5 1.8 - - - -
128B GLN* 2.7 36.4 + - - +
140B TRP* 3.5 41.4 - - - -
144B GLU* 3.4 12.6 + - - -
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Residues in contact with MET 125 (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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128A GLN* 4.7 5.4 - - - +
140A TRP* 3.4 33.0 - - + +
141A GLN* 3.5 26.7 - - - +
45B GLY 5.7 1.6 - - - +
47B LEU* 3.5 16.6 - - + +
122B ASN* 4.9 13.2 - - - +
123B TRP 3.3 0.2 - - - -
124B SER* 1.3 90.0 + - - +
126B TYR* 1.3 66.7 + - + +
128B GLN* 3.5 5.0 + - + +
129B HIS* 2.9 30.1 + - - +
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Residues in contact with TYR 126 (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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39B ASN 4.5 0.3 + - - -
40B TYR* 2.7 61.7 + + + -
44B ARG 4.5 1.2 + - - -
45B GLY* 3.3 14.7 - - - -
47B LEU* 3.6 32.3 - - + +
54B GLY* 5.1 7.7 - - - -
57B LYS* 6.1 1.1 - - - -
58B LEU* 4.1 13.3 - - + +
85B TYR* 3.8 19.3 - + + -
88B LEU* 3.5 22.1 - - + +
121B PHE* 5.0 4.0 - + - -
122B ASN 5.1 2.0 - - - -
123B TRP* 2.8 46.2 + + + +
125B MET* 1.3 79.2 - - + +
127B SER* 1.3 57.0 + - - +
129B HIS* 3.2 2.1 + - - +
130B ALA* 2.8 26.2 + - - +
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Residues in contact with SER 127 (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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88B LEU* 3.6 22.6 - - - +
113B TRP* 5.2 0.2 - - - -
123B TRP* 2.9 9.2 + - - +
124B SER* 3.5 6.3 - - - -
126B TYR* 1.3 72.7 - - - +
128B GLN* 1.3 66.0 + - - +
130B ALA* 3.2 3.1 + - - +
131B CYS* 2.9 26.9 + - - -
140B TRP* 3.8 14.4 - - - -
143B LYS* 4.6 3.2 - - - +
144B GLU* 2.7 44.7 + - - +
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Residues in contact with GLN 128 (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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128A GLN* 3.2 44.1 - - + +
129A HIS* 5.9 0.8 - - - -
131A CYS* 4.7 5.0 - - - +
132A LEU* 4.1 21.7 - - - +
138A GLU 5.6 0.2 - - - +
139A CYS* 6.5 0.4 - - - -
140A TRP* 3.9 24.3 + - + +
124B SER 2.7 20.5 + - - +
125B MET* 3.8 6.3 - - + +
127B SER* 1.3 71.7 - - - +
129B HIS* 1.3 59.9 + - - +
131B CYS* 3.1 7.7 + - - +
132B LEU* 2.8 30.9 + - + +
140B TRP* 3.6 31.3 - - + +
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Residues in contact with HIS 129 (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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137A GLY 4.6 6.7 - - - -
139A CYS* 5.1 9.0 - - + +
47B LEU* 3.3 44.0 + - + +
50B PRO* 6.5 0.4 - - + -
55B PRO* 4.1 18.9 - - + +
58B LEU* 3.8 18.8 - - + -
59B ARG* 5.8 0.2 + - - -
125B MET 2.9 18.1 + - - +
126B TYR 3.7 3.6 - - - +
128B GLN* 1.3 80.4 - - + +
130B ALA* 1.3 61.2 + - - +
132B LEU* 3.1 27.2 + - + +
133B ILE* 3.1 41.8 + - + +
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Residues in contact with ALA 130 (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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58B LEU* 4.5 8.4 - - + +
88B LEU* 3.8 25.1 - - + -
89B SER* 4.4 4.9 - - - +
126B TYR 2.8 20.2 + - - +
127B SER* 3.8 4.3 - - - +
129B HIS* 1.3 72.7 - - - +
131B CYS* 1.3 62.5 + - - +
133B ILE* 3.3 11.3 + - + +
134B GLU* 2.9 47.2 + - - +
143B LYS* 4.6 3.1 - - + +
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Residues in contact with CYS 131 (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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132A LEU* 3.9 9.9 - - + +
127B SER 2.9 15.5 + - - +
128B GLN* 3.3 13.5 - - - +
130B ALA* 1.3 78.4 - - - +
132B LEU* 1.3 62.6 + - - +
134B GLU* 4.2 6.7 - - - +
135B GLY* 3.5 14.4 + - - -
136B LYS 4.4 4.5 + - - -
137B GLY 4.8 3.3 + - - -
138B GLU* 3.2 39.6 + - - +
139B CYS 3.5 20.9 - - - -
140B TRP* 3.7 2.2 - - - -
143B LYS* 3.6 22.2 - - - -
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Residues in contact with LEU 132 (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 CYS* 3.4 35.9 - - + +
132A LEU* 3.7 16.2 - - + +
135A GLY* 5.6 4.2 - - - -
137A GLY* 3.3 42.1 - - - +
138A GLU 3.3 17.9 - - - +
139A CYS* 4.5 1.6 - - - +
128B GLN* 2.8 18.0 + - + +
129B HIS* 3.1 30.5 + - + +
131B CYS* 1.3 79.7 - - - +
133B ILE* 1.3 62.5 + - + +
135B GLY* 3.5 10.0 + - - -
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Residues in contact with ILE 133 (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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137A GLY* 5.5 5.2 - - - -
55B PRO 4.9 0.9 - - - +
58B LEU* 3.8 43.3 - - + +
59B ARG* 3.9 20.2 - - + +
62B ALA* 4.0 14.4 - - + +
89B SER* 5.7 0.2 - - - +
129B HIS* 3.1 34.3 + - + +
130B ALA* 3.7 8.3 - - + +
132B LEU* 1.3 84.0 - - + +
134B GLU* 1.3 62.9 + - - +
135B GLY* 3.1 6.2 + - - -
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Residues in contact with GLU 134 (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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62B ALA* 4.2 12.1 - - + +
89B SER* 2.9 38.1 + - - +
92B SER* 4.7 5.5 + - - -
130B ALA* 2.9 25.6 + - - +
131B CYS* 4.2 4.3 - - - +
133B ILE* 1.3 77.8 - - - +
135B GLY* 1.3 63.7 + - - +
136B LYS* 3.2 33.1 + - + +
138B GLU* 4.2 5.5 - - - +
143B LYS* 2.9 33.3 + - - -
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Residues in contact with GLY 135 (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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132A LEU 6.2 0.4 - - - -
131B CYS 3.5 3.7 + - - -
132B LEU 3.5 12.5 + - - -
133B ILE 3.1 4.9 - - - -
134B GLU* 1.3 78.7 - - - +
136B LYS* 1.3 70.8 + - - +
137B GLY 3.4 3.4 - - - -
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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