Contacts of the helix formed by residues 125 - 142 (chain A) in PDB entry 1QU3
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 LYS 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ARG 3.0 17.9 - - - +
122A GLU* 3.2 34.0 + - - +
124A CYS* 1.3 76.3 - - - +
126A GLU* 1.3 67.1 + - + +
127A PHE 4.0 1.8 - - - +
128A ALA* 3.8 6.3 - - - -
129A LEU* 3.4 30.5 + - + +
155A LEU* 3.8 32.3 - - + -
459A TRP* 3.5 11.9 - - + -
493A ASN* 5.7 1.4 + - - -
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Residues in contact with GLU 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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122A GLU* 2.8 27.9 + - + +
123A LYS* 3.8 36.9 + - + +
125A LYS* 1.3 77.5 - - + +
127A PHE* 1.3 57.2 - - - +
129A LEU* 3.0 10.2 + - - +
130A GLU* 2.6 54.1 + - + +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 4.3 2.9 - - - -
60A ASN* 3.8 31.4 - - + -
101A ILE* 3.9 22.7 - - + -
104A ALA* 4.4 21.1 - - + -
105A LEU* 4.5 19.1 - - + -
123A LYS 4.7 4.6 + - - +
124A CYS* 4.9 1.1 - - - -
125A LYS 4.8 2.7 - - - +
126A GLU* 1.3 79.0 - - - +
128A ALA* 1.3 59.1 + - - +
130A GLU* 2.6 40.5 + - - +
131A GLN* 2.8 54.0 + - + +
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Residues in contact with ALA 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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59A ALA* 3.9 10.5 - - + +
96A THR* 3.9 36.3 - - + +
101A ILE* 4.7 4.5 - - + -
124A CYS 4.8 0.6 - - - +
125A LYS* 3.8 21.5 - - - +
127A PHE* 1.3 83.5 - - - +
129A LEU* 1.3 57.8 + - + +
131A GLN* 2.7 25.6 + - - +
132A ILE* 3.0 16.9 + - - +
155A LEU* 4.4 0.9 - - + -
459A TRP* 4.5 1.3 - - + -
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Residues in contact with LEU 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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96A THR* 4.8 4.5 - - + -
125A LYS* 3.4 26.5 - - + +
126A GLU* 3.0 9.0 + - - +
128A ALA* 1.3 81.7 - - + +
130A GLU* 1.3 62.0 + - + +
131A GLN 2.9 5.8 - - - -
132A ILE* 2.6 45.1 - - + +
133A GLU* 3.2 11.1 + - - +
153A ILE* 5.4 4.3 - - + -
155A LEU* 4.2 26.5 - - + -
156A LYS* 6.5 0.4 - - - -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLU* 2.6 43.6 + - + +
127A PHE* 2.6 29.2 + - - +
129A LEU* 1.3 71.4 - - - +
131A GLN* 1.3 62.8 + - - +
133A GLU* 4.7 3.7 - - - +
134A LEU* 3.2 29.0 + - + +
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Residues in contact with GLN 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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59A ALA* 3.5 31.9 - - - +
60A ASN* 4.2 1.5 + - - +
61A GLY* 3.6 24.3 + - - +
127A PHE* 2.8 54.9 + - + +
128A ALA 2.7 11.0 + - - +
130A GLU* 1.3 88.3 + - - +
132A ILE* 1.3 65.3 + - - +
133A GLU 3.1 1.6 - - - -
134A LEU* 2.6 32.7 + - - +
135A GLN* 2.7 19.6 + - - +
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Residues in contact with ILE 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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59A ALA* 4.3 5.8 - - + +
94A TRP* 3.9 50.4 - - + +
96A THR* 4.6 2.2 - - + -
128A ALA 3.0 15.0 + - - +
129A LEU* 2.6 50.3 - - + +
131A GLN* 1.3 74.8 - - - +
133A GLU* 1.3 85.3 + - - +
135A GLN* 3.1 1.2 + - - +
136A LYS* 2.6 30.1 + - - +
151A PRO* 6.2 1.1 - - + -
153A ILE* 4.1 26.0 - - + -
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Residues in contact with GLU 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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129A LEU* 3.2 10.3 + - + +
130A GLU* 4.7 4.3 - - - +
131A GLN 3.1 0.4 - - - -
132A ILE* 1.3 112.3 - - + +
134A LEU* 1.3 58.1 + - + +
136A LYS* 2.7 60.0 + - - +
137A LYS* 3.2 8.3 + - - +
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Residues in contact with LEU 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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130A GLU 3.2 19.3 + - - +
131A GLN* 2.6 39.8 + - - +
133A GLU* 1.3 77.5 - - + +
135A GLN* 1.3 58.4 + - + +
137A LYS* 4.0 8.2 + - - +
138A ASP* 3.2 15.8 + - - +
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Residues in contact with GLN 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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57A PRO* 4.6 2.9 - - - +
58A TYR 3.5 9.2 + - - +
59A ALA* 4.1 2.8 - - - -
60A ASN 3.4 26.1 + - - +
61A GLY 2.6 32.3 + - - +
62A ASN* 4.4 1.1 - - - -
63A LEU* 3.3 35.7 - - + +
67A HIS* 5.2 0.7 + - - -
94A TRP* 3.0 30.7 + - + +
131A GLN* 2.7 20.6 + - - +
134A LEU* 1.3 74.2 - - + +
136A LYS* 1.3 64.1 + - - +
137A LYS 3.4 0.4 - - - -
138A ASP* 3.3 10.9 + - - +
139A PHE* 3.1 26.0 + - - -
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Residues in contact with LYS 136 (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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94A TRP* 3.8 23.3 - - + -
132A ILE* 2.6 20.2 + - - +
133A GLU* 2.7 48.1 + - - +
135A GLN* 1.3 67.9 - - - +
137A LYS* 1.3 66.0 + - - +
138A ASP 3.1 0.5 + - - -
139A PHE* 3.2 4.7 + - - +
140A ARG* 2.9 56.1 + - - +
148A PHE* 3.2 42.7 + - + +
149A ASN* 5.1 3.2 + - - +
151A PRO* 4.3 11.4 - - - +
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Residues in contact with LYS 137 (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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133A GLU 3.2 6.1 + - - +
134A LEU* 4.2 9.0 - - - +
135A GLN 3.4 0.4 - - - -
136A LYS* 1.3 77.4 - - - +
138A ASP* 1.3 51.9 + - - +
140A ARG* 3.2 11.4 + - + +
141A ARG* 2.5 51.0 + - - +
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Residues in contact with ASP 138 (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 ASN* 5.1 6.0 - - - +
63A LEU* 3.4 31.5 + - + +
134A LEU 3.2 18.9 - - - +
135A GLN* 3.3 13.0 - - - +
136A LYS 3.1 0.4 + - - -
137A LYS* 1.3 75.0 - - - +
139A PHE* 1.3 60.3 + - - +
141A ARG* 2.5 33.9 + - - +
142A LEU* 2.8 15.5 + - + +
606A PRO* 6.5 0.9 - - + -
607A ASP* 4.8 17.5 - - - +
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Residues in contact with PHE 139 (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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57A PRO* 4.4 4.7 - - + -
63A LEU* 3.3 40.6 - - + -
67A HIS* 3.7 20.6 - + + -
71A LYS* 3.0 54.1 - - + -
94A TRP* 3.5 32.8 - + - -
135A GLN* 3.1 18.1 + - - -
136A LYS 3.2 2.1 + - - +
138A ASP* 1.3 77.5 - - - +
140A ARG* 1.3 60.6 + - - +
142A LEU* 3.0 20.6 + - + +
144A VAL* 3.3 23.8 - - + +
148A PHE* 3.4 25.4 - + + -
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Residues in contact with ARG 140 (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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28A GLN* 3.4 18.2 - - + +
32A ASP* 5.0 19.6 + - - +
136A LYS* 2.9 46.4 + - - +
137A LYS* 3.4 11.4 - - + +
139A PHE* 1.3 71.4 - - - +
141A ARG* 1.3 54.9 + - - +
142A LEU 2.9 5.2 - - - -
143A GLY* 2.8 25.3 + - - -
144A VAL 4.5 8.8 - - - +
148A PHE* 3.6 35.0 + - + +
149A ASN* 2.8 32.7 - - - +
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Residues in contact with ARG 141 (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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21A PRO* 4.1 10.1 + - - +
24A GLU* 4.5 4.4 + - - -
25A PRO* 3.3 37.1 - - - +
28A GLN* 3.4 30.5 + - - +
137A LYS* 2.5 26.7 + - - +
138A ASP* 2.5 23.5 + - - +
140A ARG* 1.3 71.5 - - - +
142A LEU* 1.3 57.5 + - + -
143A GLY 3.2 1.3 - - - -
607A ASP* 5.8 2.5 - - - +
610A VAL* 3.2 33.0 + - + +
611A LYS* 2.7 39.9 - - - +
615A ALA* 3.7 14.7 - - - +
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Residues in contact with LEU 142 (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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63A LEU* 5.4 3.6 - - + -
65A MET* 6.1 0.7 - - + -
68A ALA* 3.9 32.1 - - + +
71A LYS* 4.9 4.7 - - + -
72A ILE* 4.3 23.9 - - + +
138A ASP* 2.8 11.7 + - + +
139A PHE* 3.3 30.3 - - + +
140A ARG 2.9 1.2 - - - -
141A ARG* 1.3 79.3 - - + +
143A GLY* 1.3 56.2 + - - +
144A VAL* 2.9 13.0 + - + +
606A PRO* 5.7 6.5 - - + -
609A VAL* 6.2 0.4 - - + -
610A VAL* 3.9 25.1 - - + -
615A ALA* 4.3 7.0 - - + -
618A ALA* 4.8 5.2 - - + -
619A ARG* 3.7 25.0 + - + -
762A HIS* 4.4 4.7 - - - -
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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
------------------------------------------------------------
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