Contacts of the helix formed by residues 122 - 132 (chain K) in PDB entry 3SWD
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 122 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91K ARG* 4.9 2.7 - - - +
94K ILE* 4.9 16.2 - - + -
111K LEU* 3.3 32.1 - - + -
112K PRO* 4.4 20.9 - - + -
120K ARG 4.2 6.3 - - - +
121K PRO* 1.3 79.2 - - - +
123K ASP* 1.3 66.1 + - - +
124K LEU 3.1 3.1 - - - -
125K HIS* 2.9 33.6 + - + +
126K ILE* 3.3 21.7 + - + +
501K EPZ 3.4 6.7 - - - -
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Residues in contact with ASP 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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121K PRO* 3.3 21.6 - - + +
122K VAL* 1.3 77.2 - - - +
124K LEU* 1.3 66.4 + - - +
126K ILE* 3.4 10.9 + - - +
127K SER* 3.0 29.2 + - - -
160K LYS* 5.2 4.2 - - - +
501K EPZ 2.9 24.2 + - - +
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Residues in contact with LEU 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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123K ASP* 1.3 86.2 - - - +
125K HIS* 1.3 62.8 + - - +
127K SER* 3.9 8.5 - - - -
128K GLY* 3.2 18.2 + - - -
158K MET* 4.2 17.7 - - + +
159K ASP* 3.9 37.7 - - + +
160K LYS* 3.7 39.0 - - + +
162K SER* 3.8 20.0 - - - -
165K ALA* 3.6 17.6 - - + +
169K ILE* 4.6 1.0 - - - +
501K EPZ 3.1 25.0 + - + +
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Residues in contact with HIS 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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94K ILE* 4.0 31.9 - - + +
95K TRP* 4.3 3.6 - - - -
97K LEU* 6.0 2.9 - - + -
122K VAL* 2.9 28.0 + - + +
124K LEU* 1.3 73.6 - - - +
126K ILE* 1.3 69.3 + - + +
128K GLY* 3.4 1.9 + - - -
129K LEU* 3.2 29.4 + - + +
164K GLY* 3.2 30.8 - - - -
165K ALA* 3.1 20.6 + - + +
168K THR* 2.6 28.9 + - + +
169K ILE* 5.3 0.6 - - - +
501K EPZ 3.5 23.6 + - - -
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Residues in contact with ILE 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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97K LEU* 5.7 3.1 - - + -
111K LEU* 5.4 5.6 - - + -
122K VAL* 3.3 27.0 + - + +
123K ASP* 3.7 9.2 - - - +
125K HIS* 1.3 77.3 - - + +
127K SER* 1.3 56.6 + - - +
129K LEU* 3.2 4.4 + - - -
130K GLU* 2.9 48.8 + - - +
136K ILE* 3.4 31.9 - - + +
143K VAL* 4.4 23.8 - - + -
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Residues in contact with SER 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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123K ASP 3.0 17.4 + - - -
124K LEU* 4.1 12.7 - - - +
125K HIS 3.3 0.2 - - - -
126K ILE* 1.3 73.5 - - - +
128K GLY* 1.3 59.5 + - - +
130K GLU* 3.4 14.6 + - - +
131K GLN* 2.9 47.3 + - - +
158K MET* 6.4 0.2 - - - -
159K ASP* 5.5 3.1 + - - -
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Residues in contact with GLY 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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124K LEU 3.2 9.1 + - - -
125K HIS 4.0 1.1 - - - -
126K ILE 3.4 0.4 - - - -
127K SER* 1.3 77.8 + - - +
129K LEU* 1.3 57.8 + - - +
131K GLN* 3.2 12.7 + - - +
132K LEU* 3.0 30.8 + - - +
156K ILE* 4.3 2.9 - - - +
158K MET* 5.4 0.6 - - - +
169K ILE* 3.3 35.7 - - - -
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Residues in contact with LEU 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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97K LEU* 3.5 38.1 - - + -
98K GLY* 4.5 8.1 - - - +
101K VAL* 5.3 6.1 - - + -
125K HIS* 3.2 14.6 + - + +
126K ILE 3.2 8.0 + - - +
128K GLY* 1.3 73.6 - - - +
130K GLU* 1.3 66.1 + - - +
132K LEU* 3.0 17.9 + - + +
133K GLY 3.4 0.5 + - - -
134K ALA* 3.2 26.2 + - + +
136K ILE* 4.0 12.3 - - + -
145K ALA* 5.2 3.8 - - + -
151K LEU* 4.6 4.4 - - + +
168K THR* 3.9 23.6 - - + +
169K ILE* 5.3 0.7 - - - -
172K ALA* 3.9 28.9 - - + -
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Residues in contact with GLU 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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126K ILE* 2.9 34.8 + - - +
127K SER* 3.8 16.6 - - - +
129K LEU* 1.3 73.2 - - - +
131K GLN* 1.3 56.4 + - - +
133K GLY* 2.8 25.3 + - - -
134K ALA 3.4 21.3 + - - +
135K THR* 5.4 0.2 - - - -
136K ILE* 3.7 25.6 + - + +
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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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127K SER* 2.9 34.2 + - - +
128K GLY 3.4 9.4 - - - +
129K LEU 3.1 0.2 - - - -
130K GLU* 1.3 78.0 - - + +
132K LEU* 1.3 58.1 + - - +
133K GLY* 3.1 5.2 + - - -
152K LYS 4.5 0.5 - - - +
154K ALA* 3.8 17.6 - - + +
155K HIS 3.8 5.5 - - - +
156K ILE* 3.1 55.6 - - + +
157K VAL 4.4 4.7 + - - +
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Residues in contact with LEU 132 (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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128K GLY 3.0 16.6 + - - +
129K LEU* 3.0 11.9 + - + +
131K GLN* 1.3 73.6 - - - +
133K GLY* 1.3 56.7 + - - +
151K LEU* 3.1 19.7 - - + +
152K LYS* 2.8 47.9 + - - +
153K GLY* 4.2 1.1 - - - -
154K ALA 3.8 7.6 - - - +
156K ILE* 4.0 13.7 - - + -
169K ILE* 3.8 23.6 - - + -
172K ALA* 4.0 25.6 - - + -
173K ALA* 4.1 11.2 - - + +
176K ALA* 5.2 1.3 - - + -
180K THR* 3.4 26.0 - - + +
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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