Contacts of the helix formed by residues 121 - 132 (chain E) in PDB entry 3SHD
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 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU* 3.1 48.5 - - + +
144D PHE* 4.2 7.8 - - + -
145D ASN* 4.4 8.3 - - - +
71E TRP* 4.9 9.4 - - + +
118E LEU* 5.6 1.8 - - + -
120E SER* 1.3 84.2 - - - +
122E LEU* 1.3 63.2 + - - +
123E VAL 3.2 0.2 - - - -
124E ALA* 3.5 8.7 + - + +
125E GLU* 3.2 20.6 + - - +
128E ARG* 4.7 3.1 + - - -
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 3.7 26.2 - - + -
69E HIS* 3.4 50.3 - - + +
71E TRP* 4.2 32.4 - - + -
81E ARG* 3.8 35.9 - - + +
120E SER* 2.8 14.7 + - - +
121E PRO* 1.3 72.6 - - - +
123E VAL* 1.3 63.2 + - - +
125E GLU* 3.7 5.5 - - + +
126E SER* 2.8 31.7 + - - -
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Residues in contact with VAL 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 5.0 3.6 - - + -
31E TRP 3.6 26.7 - - - +
32E ASN* 3.6 26.2 - - - +
33E GLN* 3.0 41.5 + - - +
81E ARG* 4.4 2.9 - - - +
112E ILE* 4.5 4.7 - - + -
118E LEU* 3.9 21.1 - - + -
119E ARG* 3.9 4.3 - - + +
120E SER* 2.9 31.9 + - - +
122E LEU* 1.3 77.7 - - - +
124E ALA* 1.3 58.6 + - - +
126E SER* 3.5 1.7 - - - -
127E ILE* 3.4 7.6 - - - +
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Residues in contact with ALA 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ILE* 4.3 7.2 - - - -
113E LEU* 3.7 24.1 - - + +
118E LEU* 3.5 22.7 - - + +
121E PRO* 3.5 9.3 + - + +
123E VAL* 1.3 77.1 - - - +
125E GLU* 1.3 59.7 + - - +
126E SER 3.0 2.2 - - - -
127E ILE* 2.8 23.4 + - - +
128E ARG* 3.1 23.8 + - - +
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 5.7 2.4 + - - -
64A HIS* 3.9 8.7 - - - -
87A GLU* 4.6 5.5 - - - +
135A ARG* 2.3 37.5 + - - -
144D PHE* 3.6 31.7 - - + -
67E ARG* 5.7 1.0 + - - -
69E HIS* 4.0 20.5 + - - +
121E PRO 3.2 15.1 + - - +
122E LEU* 3.3 8.5 + - + +
124E ALA* 1.3 77.9 - - - +
126E SER* 1.3 51.6 + - - +
128E ARG* 2.9 28.1 + - - +
129E CYS* 2.8 35.4 + - - -
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Residues in contact with SER 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E VAL* 4.2 4.9 - - - +
33E GLN* 3.1 22.6 + - - -
69E HIS* 5.2 2.2 - - - -
81E ARG* 2.8 26.0 + - - -
83E LEU* 3.6 25.4 - - - +
122E LEU* 2.8 23.6 + - - +
123E VAL 3.5 4.0 - - - -
125E GLU* 1.3 76.5 - - - +
127E ILE* 1.3 57.2 + - - +
129E CYS* 3.2 6.5 + - - +
130E TYR* 2.9 26.2 + - - +
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Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 4.9 5.6 - - + -
18E PHE* 4.8 19.3 - - + -
33E GLN* 3.3 28.9 - - - +
109E ALA* 4.2 8.3 - - + +
112E ILE* 3.7 32.8 - - + -
113E LEU* 3.8 18.6 - - + -
123E VAL 3.4 7.4 - - - +
124E ALA 2.8 9.8 + - - +
126E SER* 1.3 75.3 - - - +
128E ARG* 1.3 61.4 + - - +
130E TYR* 3.0 6.5 + - + +
131E GLN* 2.7 55.0 + - + +
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Residues in contact with ARG 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A HIS* 4.7 7.3 + - - -
87A GLU* 3.6 48.4 + - - +
89A GLU* 5.5 4.0 + - - -
130A TYR* 4.3 5.6 - - - -
133A GLY 4.8 0.9 - - - +
135A ARG* 3.7 30.0 + - - +
144D PHE* 6.0 1.2 - - - -
113E LEU* 3.9 34.6 + - + +
121E PRO 4.7 2.8 + - - -
124E ALA* 3.1 15.0 + - - +
125E GLU* 2.9 44.0 + - - +
127E ILE* 1.3 76.7 - - - +
129E CYS* 1.3 61.0 + - - +
131E GLN* 3.3 13.2 + - - +
132E SER 3.2 18.4 + - - -
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Residues in contact with CYS 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A HIS* 5.7 0.7 - - - -
135A ARG* 3.7 19.3 - - - +
66E ILE* 3.7 24.4 - - + +
67E ARG* 4.1 14.8 - - - -
69E HIS* 3.8 31.9 - - - -
83E LEU* 4.4 1.1 - - + -
125E GLU* 2.8 17.5 + - - -
126E SER* 3.4 9.2 - - - +
128E ARG* 1.3 74.7 - - - +
130E TYR* 1.3 65.0 + - - +
132E SER* 3.0 22.9 + - - -
133E GLY 4.4 0.3 + - - -
134E GLN 4.9 0.5 - - - +
135E ARG* 4.6 2.6 + - - -
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Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.2 39.0 - - + -
13E HIS* 3.0 26.8 + + + -
18E PHE* 3.6 29.6 - + + -
66E ILE* 4.6 7.5 - - + +
85E ALA* 4.6 9.2 - - + -
86E ILE 5.4 0.7 - - - -
87E GLU* 2.5 28.9 + - - -
126E SER 2.9 13.9 + - - +
127E ILE* 3.0 9.8 + - - +
129E CYS* 1.3 76.9 - - - +
131E GLN* 1.3 70.9 + - + +
132E SER 3.5 0.3 + - - -
133E GLY 3.5 3.1 + - - -
135E ARG* 3.0 56.8 + - - +
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Residues in contact with GLN 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER 4.9 2.4 - - - +
133A GLY* 3.7 25.3 - - - +
18E PHE* 5.3 2.0 - - + -
109E ALA* 3.3 28.7 - - + +
110E GLU* 4.8 4.6 + - - -
113E LEU* 3.9 12.7 - - - +
127E ILE* 2.7 37.2 + - + +
128E ARG* 3.8 13.7 - - - +
129E CYS 3.1 0.4 - - - -
130E TYR* 1.3 81.5 - - + +
132E SER* 1.3 62.7 + - - +
133E GLY* 3.2 3.5 + - - -
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Residues in contact with SER 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLY 3.5 11.0 + - - -
134A GLN* 5.4 2.3 - - - -
135A ARG* 3.8 38.7 + - - +
136A TYR* 5.6 3.5 - - - -
128E ARG 3.2 8.6 + - - -
129E CYS* 3.0 18.1 + - - -
131E GLN* 1.3 75.8 - - - +
133E GLY* 1.3 59.4 + - - +
134E GLN* 3.3 24.0 + - - +
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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