Contacts of the helix formed by residues 120 - 136 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H ILE* 2.8 34.8 + - + +
119H LEU* 1.3 87.4 - - + +
121H ASP* 1.3 64.2 + - - +
122H LEU 3.3 0.7 - - - -
123H ASP* 3.1 2.2 + - - +
124H MET* 2.8 55.9 + - + +
170H PHE* 6.1 1.6 - - + -
296H PHE* 4.2 23.3 - - + -
8001H I3E 5.2 3.1 - - + -
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Residues in contact with ASP 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLU* 4.3 12.4 - - + +
112H LYS* 2.8 46.2 + - - +
116H ILE* 3.2 19.4 + - - +
117H SER* 3.5 11.0 - - - +
120H VAL* 1.3 78.4 - - - +
122H LEU* 1.3 64.7 + - + +
124H MET* 3.3 5.5 + - - +
125H VAL* 2.9 35.4 + - + +
170H PHE* 3.5 17.9 - - - +
172H LEU* 5.7 0.9 - - + -
173H LEU* 4.5 10.1 - - + +
296H PHE* 5.3 0.7 - - - -
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Residues in contact with LEU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ILE* 3.8 29.4 - - + -
99H ARG* 3.8 32.8 - - + +
102H LEU* 4.0 17.7 - - + -
103H ALA* 3.9 17.0 - - + +
106H GLU* 5.2 0.9 - - + -
117H SER* 2.9 27.8 + - - +
118H TYR 3.7 9.9 - - - +
121H ASP* 1.3 80.4 - - + +
123H ASP* 1.3 62.7 + - - +
125H VAL* 3.5 7.7 + - + +
126H LEU* 3.1 30.3 + - + +
172H LEU* 3.6 28.0 - - + -
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Residues in contact with ASP 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ARG* 3.7 19.4 + - - +
118H TYR 4.0 3.2 + - - -
119H LEU 3.1 26.6 - - - +
120H VAL* 3.1 3.4 + - - +
122H LEU* 1.3 79.4 - - - +
124H MET* 1.3 59.0 + - + +
126H LEU* 3.3 9.1 + - - +
127H LYS* 2.8 66.6 + - - +
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Residues in contact with MET 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H VAL* 2.8 43.6 + - + +
121H ASP* 3.9 1.6 - - - +
123H ASP* 1.3 75.5 - - + +
125H VAL* 1.3 58.8 + - - +
127H LYS* 3.9 7.8 - - + +
128H CYS* 2.8 32.6 + - - +
173H LEU* 3.5 31.5 - - + +
177H TRP* 4.8 4.9 - - + +
459H PHE* 3.8 28.5 - - + +
8001H I3E 3.7 28.7 - - + -
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Residues in contact with VAL 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ILE* 4.0 36.3 - - + -
121H ASP 2.9 22.6 + - - +
122H LEU* 3.6 10.3 - - + +
124H MET* 1.3 75.0 - - - +
126H LEU* 1.3 63.7 + - - +
128H CYS* 3.7 1.2 - - - +
129H LEU* 3.1 27.7 + - + +
172H LEU* 3.6 44.6 - - + +
173H LEU* 3.6 12.5 - - - +
176H ALA* 4.1 14.8 - - + +
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ALA* 2.9 41.7 - - + +
95H ILE* 3.8 13.7 - - + -
96H GLU* 3.8 39.3 - - + +
99H ARG* 4.4 19.3 - - + +
122H LEU 3.1 21.9 + - - +
123H ASP* 3.6 8.7 - - - +
125H VAL* 1.3 80.5 - - - +
127H LYS* 1.3 59.2 + - + +
129H LEU* 4.1 0.9 - - - +
130H ARG* 3.0 50.0 + - - +
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Residues in contact with LYS 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ASP* 5.5 2.6 + - - -
82F SER* 5.3 8.5 - - - +
147G ASP* 3.7 26.9 + - - +
123H ASP* 2.8 52.4 + - - +
124H MET* 3.3 8.5 + - + +
125H VAL 3.3 0.2 - - - -
126H LEU* 1.3 74.7 - - + +
128H CYS* 1.3 56.2 + - - +
130H ARG* 4.0 5.7 - - - +
131H TYR* 2.8 36.2 + - - +
461H ALA* 4.0 9.7 - - + +
462H GLN* 6.4 0.2 - - - +
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Residues in contact with CYS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H MET 2.8 18.4 + - - +
125H VAL 3.7 4.3 - - - +
127H LYS* 1.3 74.0 - - - +
129H LEU* 1.3 66.6 + - - +
131H TYR* 3.3 1.9 + - - +
132H TYR* 3.0 49.1 + - - -
176H ALA* 3.3 35.7 - - + -
177H TRP* 3.8 25.1 - - + +
461H ALA* 4.1 12.5 - - + +
477H LEU* 4.4 4.0 - - + -
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU* 4.1 32.1 - - + +
91H LEU* 4.1 20.6 - - + -
92H ALA* 4.2 18.2 - - + -
95H ILE* 3.5 33.2 - - + -
125H VAL* 3.1 21.7 + - + +
126H LEU* 5.2 0.2 - - - -
128H CYS* 1.3 79.8 - - - +
130H ARG* 1.3 58.7 + - - +
132H TYR* 3.9 3.6 - - - +
133H ALA* 2.9 29.5 + - - +
176H ALA* 4.1 19.1 - - + -
179H LEU* 4.8 5.6 - - + -
180H GLY* 4.4 15.5 - - - +
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Residues in contact with ARG 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 3.4 50.5 - - - +
89F ASN* 6.1 0.2 - - - +
138F LYS* 4.9 0.5 + - - -
89H ASN* 3.4 24.0 + - - +
92H ALA* 3.7 25.4 + - + +
93H ASP* 2.9 27.7 + - - +
96H GLU* 2.8 30.9 + - - -
126H LEU* 3.0 38.5 + - - +
127H LYS* 4.0 5.4 - - - +
129H LEU* 1.3 73.5 - - - +
131H TYR* 1.3 68.2 + - - +
133H ALA* 3.5 2.9 + - - +
134H GLY* 3.3 14.7 + - - -
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Residues in contact with TYR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ASP* 3.3 24.0 - - - +
138F LYS* 3.0 53.9 + - + +
140F HIS* 4.5 6.1 + - - -
127H LYS 2.8 22.8 + - - +
128H CYS 3.6 2.0 - - - +
130H ARG* 1.3 73.4 - - - +
132H TYR* 1.3 79.0 + + - +
134H GLY 3.1 4.9 + - - -
135H TRP* 2.9 34.9 + + - -
461H ALA* 3.2 34.5 - - + -
462H GLN* 3.6 28.0 + - + +
478H GLY* 3.3 24.4 - - - -
479H GLU 3.5 1.9 + - - -
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Residues in contact with TYR 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU* 4.3 1.1 - - + -
128H CYS* 3.0 40.2 + - - +
129H LEU 4.2 1.3 - - - +
131H TYR* 1.3 85.0 - + - +
133H ALA* 1.3 68.3 + - - +
135H TRP* 2.9 28.8 + + + +
136H ALA 3.4 6.8 + - - -
177H TRP 5.2 0.2 - - - -
180H GLY* 3.6 24.0 - - - +
181H PRO* 3.8 34.7 - - + +
184H ALA* 3.4 12.2 - - + +
461H ALA* 5.6 0.2 - - + -
477H LEU* 2.8 49.0 + - + -
478H GLY 3.0 14.5 + - - -
481H GLY* 3.8 5.0 - - - -
482H LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H GLY* 3.4 37.4 - - - +
88H LEU* 3.7 18.9 - - + +
89H ASN* 3.6 22.4 - - - +
129H LEU 2.9 19.5 + - - +
130H ARG 3.6 7.0 - - - +
132H TYR* 1.3 75.9 - - - +
134H GLY* 1.3 62.4 + - - +
136H ALA* 3.3 8.8 + - - +
137H ASP* 5.0 1.7 - - - +
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Residues in contact with GLY 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ARG 6.1 0.2 - - - -
134F GLY* 3.8 23.6 - - - -
138F LYS* 3.8 8.3 - - - -
89H ASN* 5.3 0.6 - - - +
130H ARG 3.3 5.3 + - - -
131H TYR 3.1 10.2 + - - -
132H TYR 3.1 0.6 - - - -
133H ALA* 1.3 81.7 - - - +
135H TRP* 1.3 58.0 + - - +
136H ALA 3.5 0.3 + - - -
137H ASP* 3.7 1.0 - - - +
138H LYS* 2.8 34.3 + - - +
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Residues in contact with TRP 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F TRP* 4.8 11.4 - + - -
138F LYS* 3.3 41.9 - - + +
140F HIS* 4.3 4.0 - + - -
131H TYR* 2.9 41.7 + + - -
132H TYR* 2.9 32.3 + + + +
134H GLY* 1.3 70.5 - - - +
136H ALA* 1.3 65.6 + - - +
137H ASP 3.0 4.3 + - - -
138H LYS* 3.0 45.8 + - + -
139H TYR* 3.7 16.5 + + - +
184H ALA* 4.6 1.6 - - + -
479H GLU* 3.5 52.3 - - + +
482H LEU* 3.6 26.1 - - + +
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Residues in contact with ALA 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO* 4.8 1.7 - - - +
81H ALA* 3.3 24.9 - - - +
82H SER* 5.1 0.4 - - - -
84H ARG* 3.1 24.1 + - + -
85H GLY* 3.6 13.9 - - - +
132H TYR 3.4 3.2 + - - +
133H ALA* 3.3 15.6 + - - +
134H GLY 3.3 2.8 - - - -
135H TRP* 1.3 77.6 - - - +
137H ASP* 1.3 59.6 + - - +
138H LYS 3.9 0.2 + - - -
139H TYR* 5.0 2.4 + - - +
184H ALA* 3.4 29.9 - - + +
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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