Contacts of the helix formed by residues 113 - 129 (chain H) in PDB entry 3DHW
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 PRO 113 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107H LEU* 3.2 13.5 - - + +
111H ASN* 3.3 16.6 - - + +
112H THR* 1.3 93.2 - - - +
114H LYS* 1.3 64.7 + - - +
115H ASP 3.4 2.5 + - - -
116H GLU* 3.5 29.7 + - + +
117H VAL* 3.1 26.4 + - + +
120H ARG* 4.4 5.6 - - - +
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Residues in contact with LYS 114 (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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112H THR 4.1 3.8 + - - +
113H PRO* 1.3 71.5 - - - +
115H ASP* 1.3 65.8 + - - +
117H VAL* 3.3 16.0 + - - +
118H LYS* 3.6 13.2 + - - +
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Residues in contact with ASP 115 (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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113H PRO 3.5 0.8 - - - -
114H LYS* 1.3 76.9 - - - +
116H GLU* 1.3 65.3 - - + +
118H LYS* 3.2 17.3 + - - +
119H ARG* 3.4 26.4 + - - +
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Residues in contact with GLU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H PRO* 3.5 23.3 + - + +
114H LYS 3.3 0.4 - - - -
115H ASP* 1.3 80.0 - - + +
117H VAL* 1.3 66.8 + - - +
119H ARG* 2.9 31.5 + - - +
120H ARG* 2.6 76.2 + - + +
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Residues in contact with VAL 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H PHE* 3.7 19.0 - - + -
104H ALA* 4.5 9.2 - - + +
107H LEU* 4.2 20.2 - - + -
108H GLU* 5.0 5.2 - - + +
112H THR 5.4 0.4 - - - -
113H PRO* 3.1 33.4 + - + +
114H LYS* 3.7 9.0 - - - +
115H ASP 3.3 0.4 - - - -
116H GLU* 1.3 75.9 - - - +
118H LYS* 1.3 66.9 + - + +
121H VAL* 2.9 46.8 + - + +
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Residues in contact with LYS 118 (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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100H PHE* 4.6 13.6 - - + -
114H LYS 3.6 8.3 + - - +
115H ASP* 3.2 9.2 + - - +
116H GLU 3.1 0.6 - - - -
117H VAL* 1.3 82.8 - - + +
119H ARG* 1.3 64.6 + - - +
122H THR* 2.6 30.1 + - - +
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Residues in contact with ARG 119 (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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115H ASP* 3.4 17.3 + - - +
116H GLU* 2.9 58.3 + - - +
118H LYS* 1.3 77.4 - - - +
120H ARG* 1.4 56.0 - - - +
122H THR* 3.1 2.6 - - - -
123H GLU* 2.3 67.1 + - - +
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Residues in contact with ARG 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H LEU* 3.4 36.1 - - + +
111H ASN* 5.5 6.8 + - - +
113H PRO* 4.4 8.1 - - - +
116H GLU* 2.6 69.7 + - + +
119H ARG* 1.4 75.1 - - + +
121H VAL* 1.3 60.5 + - - +
123H GLU* 4.0 10.1 - - - +
124H LEU* 2.5 54.2 + - + +
156H ALA 3.8 12.2 + - - -
157H SER* 6.2 1.0 - - - +
158H ASN* 4.2 17.5 + - - -
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Residues in contact with VAL 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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100H PHE* 3.3 33.2 - - + +
103H VAL* 3.4 16.6 - - + +
104H ALA* 3.7 14.8 - - - +
107H LEU* 3.6 21.8 - - + -
117H VAL* 2.9 32.9 + - + +
120H ARG* 1.3 75.2 - - - +
122H THR* 1.4 53.8 + - - +
124H LEU* 3.8 0.3 - - - -
125H LEU* 2.6 65.3 + - + +
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Residues in contact with THR 122 (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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100H PHE* 4.4 11.3 - - - -
118H LYS* 2.6 24.1 + - - +
119H ARG* 3.0 3.3 + - - +
121H VAL* 1.4 78.4 - - - +
123H GLU* 1.3 54.2 + - + +
125H LEU* 3.2 9.3 + - + +
126H SER* 2.6 36.9 + - - -
131H GLY 6.1 1.1 - - - +
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Residues in contact with GLU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H ARG* 2.3 72.1 + - - +
120H ARG* 3.7 10.5 - - - +
122H THR* 1.3 67.5 - - + +
124H LEU* 1.3 71.5 + - + +
126H SER* 2.7 25.2 + - - -
127H LEU* 2.9 7.7 + - - +
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Residues in contact with LEU 124 (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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103H VAL* 4.4 2.7 - - + -
107H LEU* 5.6 0.2 - - + -
120H ARG* 2.5 63.7 + - + +
121H VAL* 4.0 2.0 - - - +
123H GLU* 1.3 77.0 - - + +
125H LEU* 1.3 57.6 + - - +
127H LEU* 2.7 30.2 + - + +
128H VAL* 2.8 17.5 + - + +
152H ALA* 2.6 37.0 - - + +
155H LEU* 3.2 42.2 - - + +
156H ALA* 3.3 6.3 - - + +
158H ASN* 5.4 6.3 - - - +
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Residues in contact with LEU 125 (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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99H VAL* 3.2 27.8 - - + -
100H PHE* 3.6 24.2 - - + +
103H VAL* 4.1 15.9 - - + -
121H VAL* 2.6 52.8 + - + +
122H THR* 3.5 7.4 - - - +
124H LEU* 1.3 75.3 - - - +
126H SER* 1.4 56.6 + - - +
128H VAL* 2.7 14.9 - - + +
130H LEU* 2.3 46.4 - - + +
131H GLY* 3.5 15.7 - - - +
135H ASP* 5.1 4.7 - - + -
149H VAL* 5.4 0.2 - - - -
152H ALA* 4.4 0.2 - - + -
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Residues in contact with SER 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR* 2.6 20.9 + - - -
123H GLU* 2.7 22.4 + - - +
125H LEU* 1.4 74.5 - - - +
127H LEU* 1.3 62.4 + - - +
128H VAL 3.6 0.2 + - - -
129H GLY* 4.0 6.4 + - - -
130H LEU 4.4 1.1 - - - -
131H GLY* 4.7 0.8 - - - -
132H ASP* 4.0 29.6 - - - +
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Residues in contact with LEU 127 (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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123H GLU 2.9 7.2 + - - +
124H LEU* 2.7 19.9 + - + +
126H SER* 1.3 84.4 + - - +
128H VAL* 1.3 60.4 + - + +
151H ILE* 6.3 0.9 - - + -
155H LEU* 4.8 18.4 - - + -
182H LEU* 4.0 18.3 - - + +
185H ASP* 6.3 2.5 - - + -
186H ILE* 5.4 8.5 - - + -
189H ARG* 6.1 2.9 - - - +
190H LEU* 4.9 17.3 - - + -
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Residues in contact with VAL 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 2.8 5.6 + - + +
125H LEU* 2.7 38.1 - - + +
127H LEU* 1.3 73.8 - - + +
129H GLY* 1.3 55.9 + - - +
130H LEU* 3.6 17.9 - - + +
148H ARG* 2.9 47.9 + - + +
151H ILE* 3.4 19.7 - - + -
152H ALA* 3.3 27.8 - - + +
155H LEU* 6.3 0.7 - - + -
182H LEU* 3.5 13.7 - - - +
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Residues in contact with GLY 129 (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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125H LEU 3.6 0.6 + - - -
126H SER 4.0 5.3 + - - -
127H LEU 3.6 2.2 - - - -
128H VAL* 1.3 80.2 - - - +
130H LEU* 1.3 64.9 + - - +
132H ASP* 4.4 10.9 + - - +
148H ARG* 3.9 20.8 + - - -
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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