Contacts of the helix formed by residues 120 - 135 (chain H) in PDB entry 3DEG
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 ASP 120 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H GLY 4.2 1.6 - - - -
119H ALA* 1.3 90.8 - - - +
121H ILE* 1.3 67.3 + - - +
122H GLU* 3.2 22.8 - - + +
123H ALA* 3.2 16.9 + - + +
124H MET* 3.2 21.4 + - - +
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Residues in contact with ILE 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H GLN* 3.7 39.9 - - + +
110H GLN* 5.5 9.0 - - + +
120H ASP* 1.3 71.5 - - - +
122H GLU* 1.3 75.2 + - - +
124H MET* 2.9 37.0 - - + +
125H THR* 2.8 23.0 + - - +
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Residues in contact with GLU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H GLN* 5.8 0.3 + - - -
120H ASP* 3.2 22.7 - - + +
121H ILE* 1.3 92.9 - - - +
123H ALA* 1.3 60.0 + - - +
125H THR* 3.2 8.7 + - - -
126H ARG* 2.9 54.0 + - - +
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Residues in contact with ALA 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080G A 3.8 1.2 + - - -
1081G U 3.4 30.5 - - - +
1082G U 4.4 2.2 - - - +
118H GLY* 4.0 11.0 - - - -
119H ALA* 4.1 0.9 - - + +
120H ASP* 3.2 20.3 + - + +
122H GLU* 1.3 78.2 - - - +
124H MET* 1.3 64.2 + - - +
126H ARG* 2.9 29.0 + - - +
127H SER* 3.1 12.8 + - - -
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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
----------------------------------------------------------
109H ALA* 3.0 37.9 - - + +
110H GLN* 4.1 3.8 - - - -
113H ALA* 4.1 17.5 - - + +
116H MET* 3.0 47.4 - - + +
118H GLY* 4.4 14.9 - - - +
119H ALA 5.7 0.2 - - - -
120H ASP* 3.2 9.7 + - - +
121H ILE* 2.9 54.3 - - + +
123H ALA* 1.3 79.1 - - - +
125H THR* 1.3 60.9 + - - +
127H SER* 3.2 3.4 + - - -
128H ILE* 3.0 12.1 + - - +
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Residues in contact with THR 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ARG* 5.0 13.5 - - + +
105H LEU* 4.0 25.8 - - + -
106H GLN* 4.0 14.6 + - + +
109H ALA* 3.9 15.1 - - - +
121H ILE* 2.8 23.4 + - - +
122H GLU* 3.4 11.8 - - - -
124H MET* 1.3 76.4 - - - +
126H ARG* 1.3 63.7 + - - +
128H ILE* 3.1 6.4 + - - +
129H GLU* 3.0 35.6 + - + +
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Residues in contact with ARG 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080G A 2.9 27.2 + - + +
1081G U 3.4 35.1 + - - -
122H GLU* 2.9 50.2 + - - +
123H ALA* 2.9 7.1 + - - +
125H THR* 1.3 75.8 - - - +
127H SER* 1.3 61.7 + - - +
129H GLU* 3.2 35.1 + - - +
130H GLY 3.3 4.9 + - - -
133H ARG* 3.6 6.2 + - - -
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Residues in contact with SER 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058G U 5.4 0.7 + - - -
1059G G 2.8 46.6 + - - +
1080G A 3.5 10.0 + - - -
1081G U 3.2 26.3 + - - -
116H MET* 3.5 16.9 - - - +
123H ALA 3.1 8.1 + - - -
124H MET* 3.4 10.1 - - - -
126H ARG* 1.3 74.7 - - - +
128H ILE* 1.3 65.8 + - - +
130H GLY 3.0 2.6 + - - -
131H THR* 3.5 4.1 + - - +
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Residues in contact with ILE 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059G G 4.3 5.8 - - - +
75H ALA* 5.2 2.5 - - + -
79H LEU* 4.0 24.3 - - + +
105H LEU* 4.1 21.1 - - + +
108H ILE* 4.1 14.8 - - + -
109H ALA* 3.8 20.0 - - + -
112H LYS* 4.0 22.4 - - + -
116H MET* 3.5 24.9 - - + -
124H MET 3.0 14.3 + - - +
125H THR 3.1 7.1 + - - +
127H SER* 1.3 76.0 - - - +
129H GLU* 1.3 59.8 + - - +
131H THR* 2.5 29.7 + - + +
132H ALA* 3.3 4.3 + - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ARG* 6.5 0.2 - - - -
105H LEU* 4.1 23.6 - - + -
125H THR* 3.0 25.1 + - - +
126H ARG* 3.2 36.7 + - - +
128H ILE* 1.3 78.2 - - - +
130H GLY* 1.3 60.2 + - - +
132H ALA* 3.1 9.1 + - - +
133H ARG* 2.9 52.6 + - - +
139H VAL* 4.9 12.0 - - + +
141H ASP* 5.5 3.1 - - - +
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Residues in contact with GLY 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059G G 3.3 9.0 - - - -
1079G C 3.0 20.0 - - - -
1088G A 3.4 5.3 + - - +
126H ARG 3.3 1.2 + - - -
127H SER 3.0 5.7 + - - -
129H GLU* 1.3 77.9 - - - +
131H THR* 1.3 57.8 + - - +
133H ARG* 2.8 24.8 + - - +
134H SER* 3.0 27.5 + - - -
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Residues in contact with THR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059G G 3.9 13.2 - - - +
1060G U 2.9 39.3 - - + +
1062G G 4.2 6.1 + - - -
1088G A 3.8 3.8 - - - +
75H ALA* 4.5 6.9 - - + +
76H ALA* 4.8 10.4 + - - -
79H LEU* 2.8 20.7 - - - +
127H SER 3.7 12.6 - - - +
128H ILE* 2.5 22.8 + - - +
130H GLY* 1.3 73.4 - - - +
132H ALA* 1.3 63.4 + - - +
134H SER* 3.3 4.9 + - - -
135H MET* 3.2 23.7 + - - +
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Residues in contact with ALA 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H LEU* 3.5 23.3 - - + -
100H ILE* 6.1 0.7 - - + -
105H LEU* 5.0 0.7 - - + -
128H ILE 4.0 4.0 - - - +
129H GLU* 3.1 12.2 + - - +
131H THR* 1.3 79.5 + - - +
133H ARG* 1.3 65.7 + - + +
135H MET* 3.0 13.1 + - - +
136H GLY 3.1 0.2 + - - -
137H LEU* 2.9 46.1 + - + +
139H VAL* 4.5 13.0 - - + -
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Residues in contact with ARG 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077G A 3.9 9.4 + - - +
1079G C 2.6 39.7 + - - +
1080G A 3.7 5.5 + - - -
92H PRO* 3.8 7.3 - - - +
93H ASN* 3.1 32.8 + - - +
126H ARG 3.6 6.1 + - - -
129H GLU* 2.9 49.0 + - - +
130H GLY* 2.8 31.2 - - - +
132H ALA* 1.3 76.8 - - + +
134H SER* 1.3 59.5 + - - +
135H MET 3.6 0.3 + - - -
136H GLY 3.9 1.2 + - - -
137H LEU 4.2 4.0 + - - +
139H VAL* 6.0 2.2 - - - +
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Residues in contact with SER 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062G G 3.0 48.4 + - - +
1063G G 3.3 7.3 - - - -
1077G A 4.5 10.6 + - - -
1088G A 3.1 29.8 + - - -
92H PRO* 3.1 11.8 - - - +
130H GLY 3.0 13.8 + - - -
131H THR 3.3 8.9 + - - -
132H ALA 3.1 1.0 - - - -
133H ARG* 1.3 77.7 - - - +
135H MET* 1.3 57.7 + - - +
136H GLY 3.5 0.9 - - - -
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Residues in contact with MET 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063G G 3.6 27.6 - - - +
76H ALA* 3.3 34.1 - - + +
79H LEU* 3.3 32.5 - - + -
80H LYS* 3.4 19.7 - - + -
85H ILE* 4.6 3.6 - - + -
88H GLY* 3.8 6.0 - - - -
89H SER* 3.2 24.1 + - - -
92H PRO* 4.4 0.4 - - - -
97H VAL* 5.2 0.3 - - - +
131H THR 3.2 8.7 + - - +
132H ALA* 3.0 15.1 + - - +
134H SER* 1.3 76.9 - - - +
136H GLY* 1.3 60.3 + - - +
137H LEU* 3.3 32.6 - - + +
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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