Contacts of the helix formed by residues 123 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.6 5.4 - - + -
40A TYR* 4.0 28.5 - + - -
82A PRO 3.5 11.2 + - - -
83A THR* 3.4 42.0 - - + -
84A VAL* 3.6 28.9 - - + +
85A TYR* 4.0 18.4 - - + -
88A LEU* 6.1 0.9 - - + -
113A TRP* 3.5 43.5 - + + +
121A PHE* 3.2 36.9 + + - +
122A ASN* 1.3 71.6 + - - +
124A SER* 1.3 54.2 + - - +
125A MET 3.2 2.7 - - - -
126A TYR* 2.7 61.7 + + + +
127A SER* 3.1 14.2 + - - +
144A GLU* 4.1 0.2 - - - -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASN* 2.9 26.5 + - - -
123A TRP* 1.3 76.2 - - - +
125A MET* 1.3 66.0 + - - +
127A SER* 3.6 1.7 - - - -
128A GLN* 2.9 46.6 + - - +
140A TRP* 3.7 28.5 - - - -
144A GLU* 3.4 15.7 + - - -
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Residues in contact with MET 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 5.6 1.6 - - - +
47A LEU* 3.6 15.7 - - + -
122A ASN* 5.2 13.5 - - - +
123A TRP 3.2 0.6 - - - -
124A SER* 1.3 89.3 + - - +
126A TYR* 1.3 63.1 - - + +
128A GLN* 3.5 17.9 - - - +
129A HIS* 3.0 38.3 + - + -
140B TRP* 3.8 15.5 - - + -
141B GLN* 3.2 31.6 - - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.1 57.8 + + + -
44A ARG 4.4 1.9 + - - -
45A GLY* 3.4 16.5 - - - -
47A LEU* 3.6 35.8 - - + +
54A GLY* 4.9 8.7 - - - -
57A LYS* 6.3 0.4 - - - -
58A LEU* 4.0 14.6 - - + +
85A TYR* 4.1 16.8 - + + -
88A LEU* 3.7 16.2 - - + +
121A PHE* 5.2 3.4 - + - -
122A ASN 5.2 1.6 - - - -
123A TRP* 2.7 44.5 + + + +
125A MET* 1.3 75.2 - - + +
127A SER* 1.3 58.9 + - - +
128A GLN 3.2 0.2 - - - -
129A HIS* 3.2 1.6 + - - +
130A ALA* 2.9 31.4 + - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.8 18.7 - - - +
123A TRP* 3.1 11.6 + - - +
124A SER 3.6 4.7 - - - -
126A TYR* 1.3 75.1 - - - +
128A GLN* 1.3 64.7 + - - +
130A ALA* 3.3 5.5 + - - +
131A CYS* 2.9 26.7 + - - -
140A TRP* 3.9 15.5 - - - -
143A LYS* 4.4 7.5 - - - +
144A GLU* 2.7 42.3 + - - +
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A SER* 2.9 35.7 + - - +
125A MET* 3.5 14.1 - - - +
127A SER* 1.3 76.9 - - - +
129A HIS* 1.3 60.7 + - + +
131A CYS* 3.1 3.6 + - - +
132A LEU* 2.9 24.9 + - - +
140A TRP* 3.2 54.6 - - + +
125B MET* 4.7 5.1 - - - +
128B GLN* 3.2 28.4 - - - +
140B TRP* 2.9 36.9 + - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.0 47.6 + - + +
48A CYS* 4.3 1.5 + - - -
55A PRO* 5.5 4.8 - - + +
58A LEU* 3.9 16.2 - - + -
125A MET* 3.0 31.3 + - + +
126A TYR 3.2 3.8 + - - +
128A GLN* 1.3 78.8 - - + +
130A ALA* 1.3 56.8 + - - +
132A LEU* 3.1 21.3 + - + +
133A ILE* 2.8 45.9 + - + +
128B GLN* 5.9 0.7 - - - -
137B GLY 4.9 4.7 + - - -
139B CYS* 3.6 30.4 - - + +
140B TRP* 6.1 2.6 - + - -
141B GLN* 5.2 1.4 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.3 9.7 - - + +
62A ALA* 6.1 0.7 - - - -
88A LEU* 3.9 27.6 - - + -
89A SER* 4.5 4.7 - - - +
126A TYR 2.9 17.8 + - - +
127A SER 3.6 4.7 - - - +
129A HIS* 1.3 74.1 - - - +
131A CYS* 1.3 59.7 + - - +
133A ILE* 4.5 7.6 - - - +
134A GLU* 2.9 48.0 + - - +
143A LYS* 4.4 3.1 - - - -
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Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A SER 2.9 18.2 + - - -
128A GLN* 3.4 10.5 - - - +
130A ALA* 1.3 76.3 - - - +
132A LEU* 1.3 62.0 + - - +
134A GLU* 4.1 3.9 - - - +
135A GLY* 3.2 17.7 + - - -
136A LYS 4.4 2.3 + - - -
137A GLY 5.1 0.2 + - - -
138A GLU* 3.2 37.9 + - - +
139A CYS 3.6 5.4 - - - -
140A TRP* 3.5 24.0 - - - +
143A LYS* 3.7 20.2 - - - +
128B GLN* 4.7 2.7 - - - +
132B LEU* 3.4 15.2 - - + +
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Residues in contact with LEU 132 (chain A).
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 2.9 8.1 + - - +
129A HIS* 3.2 44.4 - - + +
131A CYS* 1.3 78.2 - - - +
133A ILE* 1.3 65.0 + - + +
135A GLY* 3.4 10.4 + - - -
128B GLN* 4.1 21.8 - - - +
131B CYS 3.9 7.0 - - - +
132B LEU* 3.7 40.1 - - + +
135B GLY* 6.2 0.3 - - - -
137B GLY* 4.1 22.0 + - - +
138B GLU 3.4 23.3 - - - +
139B CYS* 4.5 1.1 - - - -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 4.2 9.9 - - + +
58A LEU* 3.6 34.8 - - + +
59A ARG* 4.0 28.9 - - + +
62A ALA* 3.8 22.9 - - + -
63A GLN* 5.6 3.1 - - + +
129A HIS* 2.8 30.3 + - + +
130A ALA* 4.2 3.8 - - - +
132A LEU* 1.3 73.9 - - + +
134A GLU* 1.3 68.3 + - - +
135A GLY* 3.2 1.9 + - - -
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 4.2 11.9 - - + +
89A SER* 2.7 37.4 + - - +
92A SER* 5.0 1.0 + - - -
130A ALA* 2.9 22.9 + - - +
131A CYS* 4.2 3.1 - - - +
133A ILE* 1.3 76.4 - - - +
135A GLY* 1.3 64.5 + - - +
136A LYS* 3.5 38.8 + - + +
138A GLU* 4.0 5.9 - - - +
143A LYS* 2.7 35.7 + - - -
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Residues in contact with GLY 135 (chain A).
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 3.2 12.4 + - - -
132A LEU 3.7 11.2 - - - -
133A ILE 3.2 3.3 - - - -
134A GLU* 1.3 77.1 - - - +
136A LYS* 1.3 58.4 + - - +
137A GLY 3.4 5.2 - - - -
132B LEU* 5.6 4.5 - - - -
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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