Contacts of the helix formed by residues 120 - 134 (chain D) in PDB entry 3SZ9
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 VAL 120 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ILE* 2.8 36.5 + - + +
118D TYR 3.4 0.2 - - - -
119D LEU* 1.3 84.9 - - + +
121D ASP* 1.3 80.3 + - - +
122D LEU 3.4 0.2 - - - -
123D ASP* 3.1 4.0 + - - +
124D MET* 2.9 43.7 + - - +
170D PHE* 6.0 0.4 - - + -
296D PHE* 4.2 20.6 - - + -
8001D I3E 5.1 4.0 - - + -
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Residues in contact with ASP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLU* 4.1 13.0 - - - +
112D LYS* 2.8 46.9 + - - +
116D ILE* 3.3 12.7 + - - +
117D SER* 3.5 11.0 - - - +
120D VAL* 1.3 85.7 - - - +
122D LEU* 1.3 72.6 + - + +
124D MET* 2.8 19.1 + - - +
125D VAL* 2.9 19.2 + - + +
170D PHE* 3.7 20.5 - - - +
172D LEU* 5.8 0.4 - - + -
173D LEU* 4.9 8.2 + - + +
296D PHE* 5.1 0.5 - - - -
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 3.7 30.1 - - + -
99D ARG* 3.8 36.8 - - + +
102D LEU* 4.0 15.0 - - + -
103D ALA* 3.8 21.8 - - + +
106D GLU* 5.1 2.2 - - + +
117D SER* 2.9 31.5 + - - +
118D TYR* 3.8 5.2 - - - +
121D ASP* 1.3 78.3 - - + +
123D ASP* 1.3 62.6 + - - +
125D VAL* 3.4 8.8 + - + +
126D LEU* 3.0 30.5 + - + +
172D LEU* 4.1 22.2 - - + -
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG* 3.7 22.5 + - - +
118D TYR 4.0 0.2 + - - -
119D LEU 3.3 20.8 - - - +
120D VAL 3.1 9.8 + - - +
121D ASP 3.1 0.2 - - - -
122D LEU* 1.3 78.9 - - - +
124D MET* 1.3 58.8 + - + +
126D LEU* 3.1 11.5 + - - +
127D LYS* 2.7 63.8 + - - +
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Residues in contact with MET 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6811C GAI 5.2 3.8 - - - +
120D VAL* 2.9 30.3 + - + +
121D ASP 2.8 12.9 + - - +
123D ASP* 1.3 73.1 - - + +
125D VAL* 1.3 64.5 + - - +
127D LYS* 3.8 9.8 - - + +
128D CYS* 2.9 27.4 + - - +
173D LEU* 3.7 28.7 - - + +
177D TRP* 5.4 3.4 - - + +
457D ASP 5.9 0.2 - - - +
459D PHE* 3.8 38.8 - - + +
460D GLY* 5.8 0.9 - - - -
8001D I3E 3.9 26.5 - - + -
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 4.3 25.1 - - + -
121D ASP* 2.9 17.3 + - - +
122D LEU* 3.4 12.6 - - + +
124D MET* 1.3 77.4 - - - +
126D LEU* 1.3 63.5 + - - +
128D CYS* 3.6 1.4 - - - +
129D LEU* 3.1 37.5 + - + +
172D LEU* 3.6 46.0 - - + +
173D LEU* 3.6 12.7 - - + +
176D ALA* 4.1 14.1 - - + -
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ALA* 3.1 36.2 - - + +
95D ILE* 4.0 15.0 - - + -
96D GLU* 3.6 43.5 - - + +
99D ARG* 4.5 22.2 - - + +
122D LEU* 3.0 20.8 + - + +
123D ASP* 3.1 10.7 + - - +
125D VAL* 1.3 76.6 - - + +
127D LYS* 1.3 64.8 + - + +
129D LEU* 3.5 2.1 + - + +
130D ARG* 3.1 42.8 + - - +
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 5.4 2.6 + - - -
82B SER* 5.0 8.5 - - - +
86B ARG* 6.5 0.7 - - - -
147C ASP* 3.5 29.3 + - - +
123D ASP* 2.7 48.3 + - - +
124D MET* 3.9 8.3 - - + +
125D VAL 3.3 0.2 - - - -
126D LEU* 1.3 78.2 - - + +
128D CYS* 1.3 58.2 + - - +
130D ARG* 4.2 5.0 - - - +
131D TYR* 3.0 30.5 + - - +
461D ALA* 4.0 7.1 - - + +
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Residues in contact with CYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D MET 2.9 18.1 + - - +
125D VAL* 3.6 4.5 - - - +
126D LEU 3.2 0.2 - - - -
127D LYS* 1.3 76.0 - - - +
129D LEU* 1.3 62.3 + - - +
131D TYR* 3.2 3.6 + - - +
132D TYR* 3.0 47.3 + - - -
176D ALA* 3.5 36.3 - - + -
177D TRP* 3.7 25.4 - - + +
461D ALA* 4.0 13.5 - - + -
477D LEU* 4.6 2.0 - - - -
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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
----------------------------------------------------------
88D LEU* 4.0 33.4 - - + +
91D LEU* 4.1 21.8 - - + -
92D ALA* 4.3 16.2 - - + -
95D ILE* 3.7 29.6 - - + -
125D VAL* 3.1 23.6 + - + +
126D LEU* 4.2 2.7 - - + +
128D CYS* 1.3 79.7 - - - +
130D ARG* 1.3 57.6 + - - +
132D TYR* 3.4 3.6 + - - +
133D ALA* 2.9 29.6 + - - +
176D ALA* 4.3 27.1 - - + +
179D LEU* 4.8 5.2 - - + -
180D GLY* 4.3 9.0 - - - +
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Residues in contact with ARG 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.4 50.0 - - - +
89B ASN* 5.9 1.1 + - - +
138B LYS* 4.7 0.9 + - - -
89D ASN* 3.4 25.8 + - - +
92D ALA* 3.4 31.1 + - + +
93D ASP* 3.1 26.1 + - - +
96D GLU* 2.7 31.3 + - - +
126D LEU* 3.1 37.1 + - - +
127D LYS* 4.2 4.9 - - - +
129D LEU* 1.3 75.3 - - - +
131D TYR* 1.3 64.2 + - - +
133D ALA* 3.5 2.6 + - - +
134D GLY* 3.4 13.9 + - - -
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Residues in contact with TYR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASP* 3.4 20.4 - - - +
138B LYS* 2.9 54.5 + - + +
140B HIS* 4.4 6.8 + - - -
127D LYS 3.0 20.4 + - - +
128D CYS 3.5 3.8 - - - +
130D ARG* 1.3 73.5 - - - +
132D TYR* 1.3 79.9 + + - +
134D GLY 3.1 4.0 + - - -
135D TRP* 3.1 32.8 + + - -
461D ALA* 3.2 30.5 - - + -
462D GLN* 3.4 37.6 + - + +
478D GLY* 3.3 22.7 - - - -
479D GLU 3.5 2.4 + - - -
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Residues in contact with TYR 132 (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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88D LEU* 4.1 2.9 - - + +
128D CYS* 3.0 33.1 + - - +
129D LEU 4.1 2.5 - - - +
131D TYR* 1.3 89.3 - + - +
133D ALA* 1.3 66.9 + - - +
135D TRP* 3.0 19.2 + + - +
136D ALA 3.5 0.7 + - - -
177D TRP 5.0 0.2 - - - -
180D GLY* 3.5 23.3 - - - +
181D PRO* 3.8 31.2 - - + +
184D ALA* 3.4 18.1 - - + +
461D ALA* 5.4 0.4 - - + -
477D LEU* 2.8 56.8 + - + -
478D GLY 3.0 11.1 + - - -
481D GLY* 3.9 5.4 - - - -
482D LEU* 3.7 31.9 - - + -
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Residues in contact with ALA 133 (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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85D GLY* 3.4 37.6 - - - +
88D LEU* 3.7 17.2 - - + +
89D ASN* 3.5 24.7 - - - +
129D LEU 2.9 17.0 + - - +
130D ARG 3.6 6.7 - - - +
131D TYR 3.2 0.2 - - - -
132D TYR* 1.3 77.3 - - - +
134D GLY* 1.3 60.9 + - - +
135D TRP 3.3 0.9 + - - -
136D ALA* 3.3 9.4 + - - +
137D ASP* 5.0 1.7 - - - +
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Residues in contact with GLY 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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130B ARG 6.0 0.2 - - - -
134B GLY* 3.8 17.0 - - - -
138B LYS* 3.8 14.6 - - - -
89D ASN* 5.2 0.4 - - - +
130D ARG 3.4 5.3 + - - -
131D TYR 3.1 9.9 + - - -
133D ALA* 1.3 78.4 - - - +
135D TRP* 1.3 58.9 + - - +
136D ALA 3.3 0.2 - - - -
137D ASP* 4.6 0.2 - - - -
138D LYS* 2.7 36.6 + - - +
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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
------------------------------------------------------------
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