Contacts of the helix formed by residues 118 - 124 (chain K) in PDB entry 5OGC
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 GLY 118 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K ASN* 5.6 7.4 - - - -
25K GLU* 5.5 2.5 - - - -
117K ALA* 1.3 76.1 - - - +
119K LYS* 1.3 70.5 + - - +
121K HIS* 3.2 18.8 - - - +
122K THR* 2.7 35.4 + - - -
338K PHE* 5.0 0.9 - - - -
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Residues in contact with LYS 119 (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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19K ARG* 3.3 29.8 - - + +
20K PRO* 2.7 26.1 + - - -
21K GLU 3.8 0.4 - - - -
22K ASN* 3.5 28.3 - - - +
25K GLU* 3.9 2.4 + - - -
114K ALA* 5.6 1.8 - - + -
117K ALA 3.5 3.6 + - - -
118K GLY* 1.3 82.9 + - - +
120K THR* 1.3 57.9 + - + +
122K THR* 3.5 6.0 + - - -
123K MET* 2.8 35.5 + - - +
331K ALA* 4.4 9.2 - - + -
332K VAL 3.3 25.6 - - - +
333K SER* 3.0 37.4 + - - +
338K PHE* 4.4 8.9 - - + -
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Residues in contact with THR 120 (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 TYR 4.3 2.9 - - - +
113K GLY* 3.5 25.8 - - - -
114K ALA 3.4 25.3 + - - +
115K THR 5.0 0.5 + - - -
116K GLY 3.8 2.3 + - - +
117K ALA* 3.5 20.6 - - - +
119K LYS* 1.3 73.4 - - + +
121K HIS* 1.3 68.4 + - - +
123K MET* 2.9 19.7 + - - +
124K LEU* 3.0 19.7 + - - +
226K SER* 5.4 3.3 + - - -
258K ASP* 5.6 8.3 - - - -
331K ALA* 4.1 3.8 - - + -
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Residues in contact with HIS 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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117K ALA* 3.7 24.1 - - + +
118K GLY* 3.2 20.5 + - - +
120K THR* 1.3 80.0 + - - +
122K THR* 1.3 57.7 + - - +
124K LEU 2.9 21.7 - - - +
125K GLY 4.8 0.3 - - - -
126K SER* 4.2 5.0 + - - -
221K MET* 5.9 7.0 - - - -
222K ASN 5.5 1.3 - - - -
223K ALA* 4.6 9.4 - - - +
224K THR* 3.3 36.8 + - + +
226K SER* 4.8 3.8 + - - -
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Residues in contact with THR 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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19K ARG* 3.1 21.9 + - - +
86K GLN* 2.9 12.6 - - - +
118K GLY 2.7 24.1 + - - -
119K LYS* 4.2 7.6 + - - -
121K HIS* 1.3 76.1 - - - +
123K MET* 1.3 59.0 + - - +
124K LEU 3.4 0.4 - - - -
126K SER* 3.1 22.0 - - - +
129K GLU* 3.3 26.9 - - + -
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Residues in contact with MET 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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17K ARG* 3.2 18.4 - - - +
19K ARG* 4.1 4.7 - - + +
86K GLN* 2.8 31.9 + - - -
109K VAL* 6.2 0.4 - - + -
111K ALA* 4.4 7.6 - - + -
112K TYR 3.9 9.9 - - - +
119K LYS 2.8 23.7 + - - +
120K THR* 2.9 9.8 + - - +
122K THR* 1.3 73.5 - - - +
124K LEU* 1.3 81.3 + - + +
126K SER* 5.0 0.4 - - - -
131K GLY* 5.4 0.3 - - - -
132K VAL* 4.9 4.2 + - + +
256K LEU* 6.1 2.2 - - + -
329K ILE* 3.4 49.8 - - + +
331K ALA* 3.8 25.1 - - + -
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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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86K GLN* 5.5 0.2 - - - +
111K ALA* 4.4 9.0 - - + -
112K TYR 5.8 0.2 - - - +
120K THR* 3.0 11.6 + - - +
121K HIS* 2.9 21.1 - - - +
123K MET* 1.3 111.0 - - + +
125K GLY* 1.3 59.4 + - - +
126K SER 2.9 6.4 + - - -
132K VAL* 5.7 3.1 - - + +
133K MET* 4.5 11.0 - - + +
256K LEU* 4.4 12.8 - - + -
258K ASP* 3.5 25.4 - - - +
401K 9V5 3.4 54.9 - - + +
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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