Contacts of the helix formed by residues 144 - 155 (chain K) in PDB entry 5AYZ
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 PHE 144 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18K LEU* 6.3 0.4 - - - -
22K TRP* 3.7 22.0 - + - -
107K THR* 4.0 14.1 - - + -
110K ARG* 3.9 21.5 - - + -
141K THR* 3.0 25.0 + - + +
142K PRO 3.3 0.8 - - - +
143K GLY* 1.3 78.1 - - - +
145K ARG* 1.3 65.2 + - - +
146K LEU* 3.2 3.8 - - - -
147K VAL* 3.0 53.1 + - + -
148K GLU* 3.3 38.0 + - + +
141L THR* 3.7 13.9 - - + -
142L PRO* 3.7 41.1 - - + +
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Residues in contact with ARG 145 (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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138K ARG* 3.6 24.9 + - - +
140K THR* 3.0 35.0 + - + +
141K THR 3.8 1.6 + - - -
144K PHE* 1.3 77.8 - - - +
146K LEU* 1.3 57.6 + - - +
148K GLU* 3.2 1.0 + - - +
149K LYS* 2.8 52.6 + - + +
162K TYR* 2.8 45.8 + - + +
163K ASP* 3.6 8.5 - - - +
25L GLU* 3.0 29.4 + - - +
26L ASP* 2.7 45.1 + - - +
102L ARG* 5.1 0.8 - - - +
103L VAL* 5.5 2.8 - - - +
106L ASN* 4.5 5.5 - - - +
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Residues in contact with LEU 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I PRO 5.6 1.1 - - - +
29I GLY* 4.5 12.1 - - - +
30I LEU* 3.6 31.2 - - + -
10K LEU* 3.9 11.0 - - + -
11K PRO* 5.5 1.3 - - + -
14K THR* 4.4 13.9 - - + -
15K LEU* 4.0 17.0 - - + -
18K LEU* 4.0 27.6 - - + -
59K PHE* 3.8 21.3 - - + -
144K PHE 3.1 0.8 + - - -
145K ARG* 1.3 78.5 - - - +
147K VAL* 1.3 61.8 + - - +
149K LYS* 4.2 0.7 - - - +
150K TYR* 3.1 25.8 + - - +
162K TYR* 3.2 24.2 + - + +
25L GLU* 4.4 2.0 + - - +
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Residues in contact with VAL 147 (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 LEU* 5.6 0.4 - - + -
22K TRP* 3.6 33.0 - - + -
59K PHE* 3.7 25.6 - - + -
107K THR* 4.1 7.4 - - + -
111K CYS* 3.6 34.9 - - + -
144K PHE* 3.0 41.2 + - + +
146K LEU* 1.3 78.4 - - + +
148K GLU* 1.3 57.9 + - - +
150K TYR* 3.4 2.4 + - - +
151K GLY 2.9 23.2 + - - -
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Residues in contact with GLU 148 (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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110K ARG* 5.7 1.7 - - - +
111K CYS* 5.9 0.2 - - - +
114K ILE* 3.5 33.4 - - + +
140K THR* 3.1 23.6 - - + +
141K THR* 2.7 45.7 + - - -
144K PHE* 3.3 34.8 - - + +
145K ARG 3.2 5.5 + - - +
147K VAL* 1.3 75.5 - - - +
149K LYS* 1.3 60.4 + - - +
151K GLY 3.3 0.7 + - - +
152K LEU* 3.0 32.1 + - - +
273K THR* 4.0 14.2 - - + +
141L THR* 4.8 0.7 - - - +
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Residues in contact with LYS 149 (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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30I LEU* 4.5 5.8 - - + -
137K THR 2.9 32.7 + - - +
138K ARG* 4.3 1.7 - - - +
140K THR* 4.4 6.9 - - + +
145K ARG* 2.8 49.2 + - + +
146K LEU 4.2 1.3 - - - +
148K GLU* 1.3 69.0 - - - +
150K TYR* 1.3 63.9 + - - +
152K LEU* 3.2 13.7 + - + +
153K LEU* 3.1 26.8 + - - +
159K SER* 2.8 42.3 + - - +
160K HIS* 4.4 0.8 - - - +
161K ARG 3.2 21.9 + - - +
162K TYR* 3.7 24.0 + - + -
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Residues in contact with TYR 150 (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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30I LEU* 5.1 5.0 - - + +
3K ALA 4.2 2.3 + - - -
6K LEU* 3.7 31.6 - - + -
7K ALA* 4.0 8.8 + - - +
9K LEU* 5.1 7.2 - - + -
10K LEU* 3.9 28.0 - - + -
56K GLY* 3.9 11.7 - - - -
58K PRO* 3.6 17.4 - - + +
59K PHE* 3.8 20.0 - + + -
77K GLU* 2.4 37.7 + - - +
111K CYS* 3.9 7.4 - - - -
146K LEU 3.1 19.3 + - - +
147K VAL 3.6 2.7 - - - +
149K LYS* 1.3 76.0 - - - +
151K GLY* 1.3 63.2 + - - +
153K LEU* 3.2 11.4 + - + +
154K VAL* 3.0 42.6 + - + +
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Residues in contact with GLY 151 (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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111K CYS* 4.0 25.6 - - - -
114K ILE* 3.9 9.2 - - - -
115K ALA* 3.1 26.3 - - - +
147K VAL 2.9 16.2 + - - -
148K GLU 3.3 3.3 + - - -
149K LYS 3.2 0.6 - - - -
150K TYR* 1.3 74.6 - - - +
152K LEU* 1.3 64.8 + - - +
154K VAL* 4.5 1.8 - - - -
155K GLY 3.2 6.8 + - - -
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Residues in contact with LEU 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K ILE* 3.7 14.0 - - + +
118K ALA* 3.9 8.4 - - + +
136K GLY* 3.5 28.3 - - - +
137K THR 4.7 1.6 - - - +
140K THR* 6.0 0.2 - - + -
148K GLU 3.0 19.1 + - - +
149K LYS* 3.2 17.0 + - + +
151K GLY* 1.3 76.9 - - - +
153K LEU* 1.3 63.3 + - - +
155K GLY 3.3 4.7 + - - -
157K ALA* 2.9 28.2 + - + +
158K ALA 4.3 10.3 - - - +
159K SER* 4.3 12.6 - - - +
272K LEU* 3.7 41.1 - - + -
273K THR* 4.3 11.9 - - + -
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Residues in contact with LEU 153 (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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30I LEU* 4.1 20.4 - - + -
32I TYR* 5.2 4.3 - - + -
190J GLN* 6.2 1.8 - - - +
191J ALA 5.9 2.9 - - - +
6K LEU* 3.8 21.0 - - + +
9K LEU* 3.5 30.7 - - + -
149K LYS 3.1 12.3 + - - +
150K TYR* 3.2 10.9 + - + +
152K LEU* 1.3 76.5 - - - +
154K VAL* 1.3 65.2 + - - +
156K GLY* 2.9 15.9 + - - -
157K ALA 3.4 15.7 - - - +
158K ALA* 4.5 2.0 - - - -
159K SER* 3.7 25.1 - - - +
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Residues in contact with VAL 154 (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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3K ALA* 4.1 13.1 - - + +
6K LEU* 3.7 16.4 - - + -
53K VAL* 4.4 5.2 - - + +
54K LEU 3.7 23.3 - - - +
55K ALA* 3.7 13.5 - - + -
77K GLU* 4.1 5.8 - - + +
78K GLY* 3.9 16.2 - - - +
115K ALA* 4.2 2.9 - - + -
150K TYR* 3.0 51.3 + - + +
151K GLY 3.9 4.7 - - - +
152K LEU 3.4 0.2 - - - -
153K LEU* 1.3 75.5 - - - +
155K GLY* 1.3 58.0 + - - +
156K GLY 3.3 3.1 + - - -
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Residues in contact with GLY 155 (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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53K VAL* 4.9 3.6 - - - -
115K ALA* 3.4 26.0 - - - +
118K ALA* 3.5 5.5 - - - +
119K ALA* 3.2 31.3 + - - +
122K VAL* 4.0 2.6 - - - +
151K GLY 3.2 10.5 + - - -
152K LEU 3.8 2.7 - - - -
153K LEU 3.1 1.2 - - - -
154K VAL* 1.3 76.2 - - - +
156K GLY* 1.3 58.8 + - - +
157K ALA 3.4 2.7 - - - -
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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