Contacts of the helix formed by residues 124 - 139 (chain D) in PDB entry 3U1K
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 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D GLN* 3.7 12.0 + - - -
123D THR* 1.3 76.7 - - - +
125D ASP* 1.3 65.8 + - - +
126D LYS* 3.6 5.0 + - - +
127D GLU* 2.8 46.6 + - - +
128D ILE* 3.2 13.0 + - - +
415D ILE* 3.5 34.8 - - - +
416D ASN* 3.9 7.2 - - - +
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Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D THR 5.1 1.0 - - - +
124D SER* 1.3 70.5 - - - +
126D LYS* 1.3 66.9 + - - +
128D ILE* 3.3 3.8 + - - +
129D LEU* 2.9 37.1 + - + +
416D ASN* 3.1 32.8 + - - +
419D LYS* 4.7 13.7 + - - -
448D LEU* 3.8 38.1 - - + +
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Residues in contact with LYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D TYR* 4.6 9.9 + - + +
104D GLN* 4.1 18.8 - - - +
124D SER* 3.3 8.4 + - - +
125D ASP* 1.3 79.9 - - - +
127D GLU* 1.3 53.5 + - - +
129D LEU* 3.7 7.8 - - + +
130D THR* 2.8 57.2 + - - +
164D GLU* 4.6 7.6 + - - -
165D PRO* 5.6 2.2 - - - +
166D ASP* 3.0 35.2 + - - +
192D ARG* 5.7 0.2 - - - +
415D ILE 5.8 2.2 - - - +
416D ASN* 4.8 0.4 + - - -
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TYR* 3.5 22.8 - - + +
103D ARG* 3.2 10.9 - - - +
104D GLN* 2.8 51.1 + - + +
123D THR* 3.3 22.0 - - + +
124D SER* 2.8 45.8 + - - +
126D LYS* 1.3 77.1 - - - +
128D ILE* 1.3 58.2 + - - +
130D THR* 3.9 1.2 - - - -
131D SER* 2.8 34.3 + - - -
445D ARG* 5.1 0.2 - - - -
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D THR* 3.6 38.4 - - + +
124D SER 3.2 9.2 + - - +
125D ASP* 3.9 4.3 - - - +
127D GLU* 1.3 75.5 - - - +
129D LEU* 1.3 63.7 + - - +
131D SER* 3.3 2.8 + - - -
132D ARG* 2.9 32.0 + - - +
443D LEU 5.7 3.8 - - - +
444D ASN 6.2 0.2 - - - -
445D ARG* 3.8 58.6 - - + +
448D LEU* 4.6 23.1 - - + -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASP* 2.9 30.7 + - + +
126D LYS* 3.8 6.3 - - - +
128D ILE* 1.3 76.9 - - - +
130D THR* 1.3 60.6 + - - +
132D ARG* 3.3 11.0 + - + +
133D ILE* 3.0 33.4 + - + +
448D LEU* 4.0 12.1 - - + -
449D GLY* 3.9 21.8 - - - +
452D ALA* 3.8 33.4 - - + -
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Residues in contact with THR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D TYR* 3.4 37.9 - - + -
126D LYS* 2.8 51.8 + - - +
129D LEU* 1.3 72.7 - - - +
131D SER* 1.3 63.9 + - - +
133D ILE* 3.0 13.2 + - + +
134D ILE* 2.9 32.1 + - + +
166D ASP* 3.7 23.5 - - + +
170D ILE* 5.8 0.7 - - + -
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 3.4 28.2 + - - +
102D TYR* 2.8 30.7 + - - +
127D GLU 2.8 24.1 + - - -
128D ILE 3.4 5.2 - - - -
130D THR* 1.3 76.6 - - - +
132D ARG* 1.3 57.4 + - - +
134D ILE* 3.4 3.2 + - - +
135D ASP* 2.9 28.6 + - - +
445D ARG* 3.4 22.1 + - - -
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D CIT 2.8 54.9 + - - -
128D ILE* 2.9 27.5 + - + +
129D LEU* 3.5 12.1 - - + +
130D THR 3.2 0.2 - - - -
131D SER* 1.3 75.5 - - - +
133D ILE* 1.3 59.2 + - - +
135D ASP* 3.2 8.7 + - - +
136D ARG* 2.9 54.8 + - - +
445D ARG* 3.6 26.5 + - + +
446D ARG* 3.5 26.7 - - - +
449D GLY* 4.0 15.6 - - - -
450D HIS* 4.2 7.1 + - - -
558D GLN* 4.8 2.4 + - - +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.0 24.7 + - + +
130D THR* 3.0 11.2 + - + +
132D ARG* 1.3 74.3 - - - +
134D ILE* 1.3 63.2 + - + +
136D ARG* 3.3 24.4 + - - +
137D SER* 3.0 26.0 + - - -
166D ASP* 6.0 3.8 - - + +
170D ILE* 3.7 20.0 - - + -
192D ARG* 5.8 2.9 - - - +
217D VAL* 4.5 11.2 - - + -
228D MET* 3.6 27.1 - - + +
230D GLU* 4.0 22.9 - - + -
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Residues in contact with ILE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 3.6 20.9 - - + -
102D TYR* 4.0 7.4 - - + -
130D THR* 2.9 30.0 + - + +
131D SER 3.7 6.1 - - - +
133D ILE* 1.3 74.9 - - - +
135D ASP* 1.3 64.8 + - - +
137D SER* 3.0 17.3 + - - -
138D ILE* 3.1 16.7 + - + +
152D VAL* 4.7 1.1 - - + -
154D CYS* 3.9 15.7 - - - -
169D ALA* 3.8 27.6 - - + -
170D ILE* 3.7 24.9 - - + -
173D ALA* 3.8 28.5 - - + -
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Residues in contact with ASP 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.9 8.9 - - - +
99D VAL* 4.8 0.3 - - - -
100D VAL* 3.8 24.5 + - + +
131D SER 2.9 19.0 + - - +
132D ARG* 3.4 9.6 - - - +
134D ILE* 1.3 77.4 - - - +
136D ARG* 1.3 58.4 + - - +
138D ILE* 3.7 1.7 - - - +
139D ARG* 2.8 76.7 + - - +
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D CIT 4.4 7.3 + - - -
132D ARG* 2.9 54.9 + - - +
133D ILE* 3.7 23.1 - - - +
135D ASP* 1.3 78.6 + - - +
137D SER* 1.3 60.1 + - - +
139D ARG* 4.9 2.9 - - - -
140D PRO* 3.3 21.2 - - - +
227D VAL* 3.9 6.1 - - - +
228D MET* 3.7 20.9 - - + +
229D LEU 5.4 0.2 + - - -
230D GLU* 2.9 33.2 + - - +
558D GLN* 3.8 23.0 + - - +
559D ALA 4.6 2.0 + - - +
560D ASP* 3.3 45.5 - - - +
561D ILE 5.1 2.0 + - - +
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Residues in contact with SER 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.0 15.1 + - - +
134D ILE 3.0 9.8 + - - -
136D ARG* 1.3 77.7 - - - +
138D ILE* 1.3 60.8 + - - +
141D LEU* 4.6 0.3 - - - +
170D ILE* 3.7 26.9 - - - +
188D VAL* 3.7 20.1 - - - +
219D ALA* 3.5 11.0 - - - +
227D VAL* 3.6 16.6 - - - +
228D MET* 3.4 29.8 - - - +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.2 13.9 - - + -
100D VAL* 4.1 16.4 - - + -
134D ILE* 3.1 13.9 + - + +
135D ASP 3.7 4.0 - - - +
137D SER* 1.3 87.3 - - - +
139D ARG* 1.3 71.0 + - - +
140D PRO* 3.3 3.8 - - - -
141D LEU* 3.2 6.9 + - - +
142D PHE* 3.6 4.3 - - + -
152D VAL* 3.8 28.9 - - + -
170D ILE* 5.0 2.7 - - + +
173D ALA* 4.0 22.9 - - + -
174D SER* 4.7 4.7 - - - +
177D LEU* 3.9 11.4 - - + -
184D TRP* 2.9 44.3 + - + +
188D VAL* 5.7 1.3 - - + -
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Residues in contact with ARG 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D MET* 3.9 26.2 + - - +
98D LEU* 2.9 47.3 + - + +
135D ASP* 2.8 56.3 + - - +
136D ARG* 4.9 2.0 - - - -
138D ILE* 1.3 78.7 - - - +
140D PRO* 1.3 66.0 - - + +
141D LEU 3.0 5.4 + - - -
142D PHE* 3.3 19.5 + - + +
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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