Contacts of the helix formed by residues 120 - 131 (chain K) 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 SER 120 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32K ASN* 5.1 2.1 + - - -
71K TRP* 3.9 24.1 - - - -
81K ARG* 5.5 1.9 + - - -
118K LEU* 3.2 11.2 - - - +
119K ARG* 1.3 81.9 - - - +
121K PRO* 1.3 76.0 - - - +
122K LEU* 2.9 24.4 + - - +
123K VAL* 3.0 23.8 + - - +
124K ALA 4.3 0.2 + - - -
158K SO4 5.2 6.8 + - - -
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Residues in contact with PRO 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 4.5 11.2 - - + -
145F ASN* 4.5 13.2 - - - +
71K TRP* 4.2 24.5 - - + +
118K LEU* 5.3 3.8 - - + -
120K SER* 1.3 87.6 - - - +
122K LEU* 1.3 63.0 + - - +
123K VAL 3.1 0.7 - - - -
124K ALA* 3.2 11.2 + - + +
125K GLU* 3.0 23.2 + - - +
128K ARG* 5.0 0.5 + - - -
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Residues in contact with LEU 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 3.4 37.0 - - + -
69K HIS* 4.2 24.0 - - + +
71K TRP* 3.7 46.2 - - + -
79K PHE* 5.7 0.7 - - + -
81K ARG* 3.7 38.1 - - + +
120K SER* 2.9 13.9 + - - +
121K PRO* 1.3 76.1 - - - +
123K VAL* 1.3 56.0 + - - +
124K ALA 3.4 0.2 - - - -
125K GLU* 3.4 5.9 - - + +
126K SER* 2.7 40.8 + - - -
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Residues in contact with VAL 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K VAL* 5.1 5.8 - - + -
31K TRP 3.7 15.0 - - - +
32K ASN* 3.5 27.8 - - - +
33K GLN* 3.0 45.6 + - - +
81K ARG* 5.2 0.4 - - - +
112K ILE* 4.1 15.9 - - + -
118K LEU* 4.1 15.9 - - + -
119K ARG 4.1 1.1 - - - +
120K SER* 3.3 26.0 - - - +
122K LEU* 1.3 73.9 - - - +
124K ALA* 1.3 68.8 + - - +
126K SER 3.3 3.8 + - - -
127K ILE* 3.5 6.9 + - - +
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Residues in contact with ALA 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K ILE* 4.4 6.3 - - - +
113K LEU* 3.8 20.2 - - + +
118K LEU* 3.8 20.4 - - + +
121K PRO* 3.2 9.7 + - + +
123K VAL* 1.3 75.8 - - - +
125K GLU* 1.3 66.3 + - - +
127K ILE* 2.7 18.9 + - - +
128K ARG* 3.0 31.3 + - - +
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 3.3 52.1 - - + -
67K ARG* 5.9 0.2 + - - -
69K HIS* 4.2 18.5 + - + +
121K PRO 3.0 11.1 + - - +
122K LEU* 3.4 12.3 - - + +
124K ALA* 1.3 77.6 - - - +
126K SER* 1.3 54.6 - - - +
128K ARG* 2.8 42.3 + - - +
129K CYS* 2.7 43.6 + - - -
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Residues in contact with SER 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 3.9 5.1 - - - +
33K GLN* 3.3 26.4 + - - -
69K HIS* 5.0 2.0 - - - -
81K ARG* 2.9 23.2 + - - -
83K LEU* 3.3 34.2 - - - +
122K LEU 2.7 24.2 + - - -
124K ALA 3.0 0.4 + - - -
125K GLU* 1.3 74.2 - - - +
127K ILE* 1.3 55.9 + - - +
129K CYS* 3.5 2.9 + - - +
130K TYR* 3.0 27.5 + - - +
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Residues in contact with ILE 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 4.8 6.3 - - + -
18K PHE* 3.7 39.9 - - + -
33K GLN* 4.4 7.6 - - - +
109K ALA* 4.0 14.8 - - + +
112K ILE* 3.7 35.2 - - + -
113K LEU* 3.9 23.1 - - + -
123K VAL 3.5 5.6 + - - +
124K ALA 2.7 11.2 + - - +
126K SER* 1.3 72.3 - - - +
128K ARG* 1.3 68.4 + - - +
130K TYR* 3.2 3.4 + - - +
131K GLN* 3.0 46.9 + - + +
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Residues in contact with ARG 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LEU* 4.0 31.3 + - + +
121K PRO 5.0 0.6 + - - -
124K ALA* 3.0 30.8 + - - +
125K GLU* 2.8 38.8 + - - +
127K ILE* 1.3 77.1 - - - +
129K CYS* 1.3 66.1 + - - +
131K GLN* 3.4 17.3 + - - +
132K SER* 3.3 15.8 + - - -
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Residues in contact with CYS 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K ILE* 3.9 20.6 - - + -
67K ARG* 4.2 17.9 - - - -
69K HIS* 3.7 30.7 - - - -
83K LEU* 4.4 2.9 - - + -
125K GLU* 2.7 23.6 + - - +
126K SER 3.6 5.4 - - - +
128K ARG* 1.3 76.0 - - - +
130K TYR* 1.3 56.0 + - - +
132K SER* 2.5 41.8 + - - -
133K GLY 3.9 0.2 + - - -
134K GLN* 4.1 9.4 - - - +
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Residues in contact with TYR 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 4.2 9.1 + - - -
11K VAL* 3.4 34.1 - - + -
13K HIS* 3.0 32.8 + + + -
18K PHE* 3.7 23.3 - + + -
66K ILE* 4.4 12.0 - - + +
85K ALA* 4.8 15.5 - - + -
86K ILE 5.9 0.4 - - - -
87K GLU* 2.7 31.9 + - - -
126K SER 3.0 15.8 + - - +
127K ILE* 3.2 6.9 + - - +
129K CYS* 1.3 79.6 - - - +
131K GLN* 1.3 65.4 + - + +
133K GLY* 3.2 19.1 + - - -
134K GLN 4.9 1.9 - - - +
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Residues in contact with GLN 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE* 5.5 1.3 - - + -
109K ALA* 3.6 26.4 - - + +
110K GLU* 5.4 2.0 + - - -
113K LEU* 4.2 10.6 - - - +
127K ILE* 3.0 30.1 + - + +
128K ARG* 3.7 20.6 - - - +
129K CYS 2.9 0.2 + - - -
130K TYR* 1.3 83.6 - - + +
132K SER* 1.3 64.5 + - - +
133K GLY* 3.0 3.4 + - - -
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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