Contacts of the helix formed by residues 121 - 128 (chain L) in PDB entry 6AHU
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 LYS 121 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146D LYS* 5.6 10.1 - - - +
181D ASN* 5.9 1.4 - - - +
219D ASP* 3.3 43.5 - - - +
220D LEU* 4.8 1.4 - - - +
2J ALA 4.5 1.4 - - - +
226J ARG* 4.1 22.0 - - - +
120L ASP* 1.3 77.9 - - - +
122L ASP* 1.3 62.1 + - - +
123L THR 3.4 0.5 + - - -
124L TYR* 4.7 0.9 - - - +
125L GLU* 3.1 47.7 + - + +
141L ILE 3.8 20.9 + - - +
142L MET* 3.2 19.6 + - + +
144L PHE* 4.5 21.4 - - + -
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Residues in contact with ASP 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LYS* 4.1 11.3 + - - +
220D LEU 3.8 8.3 - - - +
2J ALA 5.5 0.7 + - - -
3J VAL* 4.1 17.7 - - - +
226J ARG* 2.4 41.0 + - - +
120L ASP* 3.3 13.7 + - - +
121L LYS* 1.3 77.3 - - - +
123L THR* 1.3 59.5 + - - +
125L GLU 4.7 0.7 - - - -
126L GLU* 3.3 32.5 - - - +
173L LYS* 5.2 0.5 + - - -
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Residues in contact with THR 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ASN* 2.8 34.8 + - - +
119L LEU* 3.7 18.6 - - + -
120L ASP* 2.9 15.0 + - - -
121L LYS 3.2 0.2 - - - -
122L ASP* 1.3 80.1 - - - +
124L TYR* 1.3 60.2 + - - +
125L GLU 3.2 1.8 - - - -
126L GLU* 3.1 4.9 + - - -
127L THR* 3.0 39.2 + - + -
173L LYS* 4.6 7.5 - - - -
175L LEU* 3.8 24.4 - - + +
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Residues in contact with TYR 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A G 5.9 1.9 - - - -
145D SER 5.9 0.2 - - - -
146D LYS 4.6 10.3 - - - -
148D PRO* 3.3 27.1 - - + +
119L LEU* 4.2 11.1 - - + +
120L ASP 3.1 18.4 + - - +
121L LYS 4.7 1.6 - - - +
123L THR* 1.3 77.0 - - - +
125L GLU* 1.3 68.5 + - + +
126L GLU 3.7 0.2 + - - -
127L THR* 3.8 6.1 + - - -
128L GLY* 3.7 15.6 + - - -
129L LEU 3.2 19.1 + - - +
131L GLY* 3.1 38.0 + - - -
132L HIS* 4.9 0.2 - - - -
144L PHE* 3.6 55.0 - + + -
146L VAL* 3.7 17.7 - - + -
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D THR 3.2 11.9 - - - +
144D LYS* 3.4 13.1 - - + +
145D SER 3.4 26.9 - - - +
146D LYS* 4.7 7.8 - - - +
151D VAL* 3.3 22.5 - - - +
220D LEU* 3.3 48.0 - - - +
121L LYS* 3.1 47.5 + - + +
122L ASP 5.3 0.2 - - - +
123L THR 3.2 0.4 - - - -
124L TYR* 1.3 86.8 - - + +
126L GLU* 1.3 60.3 + - + +
128L GLY 4.5 0.4 - - - -
144L PHE* 6.1 0.4 - - + -
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Residues in contact with GLU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D THR* 3.3 26.4 + - - +
144D LYS* 3.3 28.3 + - + -
151D VAL* 3.7 3.4 - - - +
122L ASP* 3.3 18.7 - - - +
123L THR 3.1 7.5 + - - +
125L GLU* 1.3 77.9 - - - +
127L THR* 1.3 64.0 + - - +
128L GLY 3.4 0.4 - - - -
172L LYS* 3.5 24.7 - - - +
173L LYS* 2.9 45.8 + - + +
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Residues in contact with THR 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L LEU* 3.9 14.8 - - + +
123L THR* 3.0 33.1 + - + +
124L TYR* 3.8 5.5 + - - -
126L GLU* 1.3 77.7 - - - +
128L GLY* 1.3 63.7 + - - +
129L LEU* 3.9 18.0 + - - +
168L SER* 2.5 31.5 + - - +
169L PHE* 4.6 7.9 - - + -
172L LYS* 3.2 14.5 + - - -
173L LYS* 3.9 22.2 - - + -
175L LEU* 4.2 8.7 - - + -
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Residues in contact with GLY 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PRO* 3.3 35.9 - - - +
151D VAL* 4.1 12.8 - - - -
124L TYR 3.7 8.1 + - - -
126L GLU 3.4 2.8 - - - +
127L THR* 1.3 81.0 + - - +
129L LEU* 1.3 64.8 + - - +
130L GLN* 4.4 1.0 + - - +
164L ARG* 4.0 16.1 + - - +
168L SER* 5.6 0.2 - - - -
172L LYS* 4.2 2.0 - - - -
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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