Contacts of the helix formed by residues 137 - 153 (chain B) in PDB entry 1YLA
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 ASN 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLN* 2.8 27.6 + - + +
136B GLN* 1.3 77.9 - - + +
138B PRO* 1.3 60.2 - - - +
139B GLU* 3.8 8.1 + - - +
140B MET* 3.3 45.8 + - + +
141B PHE 3.0 20.1 + - - -
187B SER* 5.9 0.8 - - - +
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Residues in contact with PRO 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLN 3.7 0.2 - - - -
134B TYR 3.7 16.6 - - - +
135B LYS 3.9 8.5 - - - +
136B GLN 3.6 7.9 - - - +
137B ASN* 1.3 88.7 - - - +
139B GLU* 1.3 59.5 + - + +
141B PHE* 3.4 6.9 + - + +
142B LYS* 3.0 44.1 + - - +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASN* 3.3 7.4 + - - +
138B PRO* 1.3 79.1 - - + +
140B MET* 1.3 65.0 + - - +
142B LYS* 3.5 31.0 + - - +
143B GLN* 3.2 36.1 + - + +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 3.6 21.1 - - - +
137B ASN* 3.3 37.9 + - + +
139B GLU* 1.3 75.6 - - - +
141B PHE* 1.3 61.4 + - - +
143B GLN* 3.3 1.4 + - - -
144B THR* 2.8 37.8 + - - +
162B TYR* 3.7 19.9 + - + +
187B SER* 3.2 53.8 - - - +
188B TRP* 4.0 11.0 - - + -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 4.8 8.7 - - + -
51B TYR* 3.6 24.0 - + - -
80B TRP* 3.5 25.8 - + - -
82B PRO* 3.7 7.6 - - + -
130B VAL* 3.5 30.5 - - + -
133B GLN* 3.3 12.3 + - - +
134B TYR* 3.4 54.5 - + + -
137B ASN 3.0 14.3 + - - +
138B PRO* 3.6 10.3 - - + +
139B GLU 3.3 0.2 - - - -
140B MET* 1.3 77.6 - - - +
142B LYS* 1.3 64.8 + - + +
144B THR* 3.8 0.3 - - - -
145B ALA* 2.8 36.3 + - + +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 3.8 16.8 - - + +
138B PRO* 3.0 38.9 + - - +
139B GLU* 3.5 31.4 + - - +
140B MET 3.3 0.2 - - - -
141B PHE* 1.3 85.5 - - + +
143B GLN* 1.3 63.3 + - - +
146B ARG* 3.0 36.3 + - - +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLU* 3.2 28.2 + - + +
140B MET* 4.7 0.2 - - - -
141B PHE 3.2 0.8 - - - -
142B LYS* 1.3 80.0 - - - +
144B THR* 1.3 59.7 + - - +
146B ARG* 3.4 35.6 + - - +
147B LEU* 3.1 26.2 + - - +
158B SER* 3.6 12.8 + - - -
159B SER* 3.3 23.4 + - - +
162B TYR* 3.5 28.6 - - + +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TRP* 3.4 30.5 - - + +
133B GLN* 3.6 12.8 + - - +
140B MET* 2.8 22.6 + - - +
141B PHE 3.8 0.2 - - - -
143B GLN* 1.3 75.3 - - - +
145B ALA* 1.3 60.9 + - - +
147B LEU* 3.2 4.0 + - - +
148B TRP* 2.8 39.5 + - + -
162B TYR* 3.9 5.1 - - - -
184B SER* 3.7 25.1 - - - +
188B TRP* 2.8 26.8 + - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 3.4 26.4 - - + +
51B TYR* 3.9 12.4 - - + +
80B TRP* 3.7 32.3 - - + +
141B PHE* 2.8 22.5 + - + +
144B THR* 1.3 77.6 - - - +
146B ARG* 1.3 55.5 + - - +
148B TRP* 3.3 2.9 + - - +
149B ALA* 2.9 28.6 + - - +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR 4.9 2.2 - - - +
50B PRO* 3.4 33.2 - - + +
142B LYS* 3.0 20.0 + - - +
143B GLN* 3.4 27.7 + - - +
144B THR 3.2 0.2 - - - -
145B ALA* 1.3 74.7 - - - +
147B LEU* 1.3 63.1 + - - +
149B ALA* 3.6 2.1 + - - +
150B HIS* 3.2 20.4 + - - +
155B ALA* 5.1 1.2 - - - +
156B PRO 4.6 1.6 - - - +
157B VAL 4.9 3.4 + - - -
158B SER* 3.4 32.2 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLN 3.1 19.9 + - - +
144B THR 3.2 4.7 + - - +
146B ARG* 1.3 73.0 - - - +
148B TRP* 1.3 76.5 + - + +
150B HIS* 3.2 6.6 + - - +
151B VAL* 3.0 34.3 + - + +
158B SER* 3.2 28.5 - - - +
162B TYR* 3.8 17.9 - - + -
163B THR* 3.9 16.2 - - + -
166B ILE* 3.6 15.9 - - + -
180B ILE* 4.6 4.7 - - + -
188B TRP* 3.3 36.3 - - + -
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Residues in contact with TRP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 4.1 17.8 - - + +
79B ILE* 3.5 34.3 - - - -
80B TRP* 3.5 34.5 - + + +
86B SER* 3.3 37.9 - - - -
144B THR* 2.8 33.8 + - + +
145B ALA 3.7 4.7 - - - +
147B LEU* 1.3 84.0 - - + +
149B ALA* 1.3 57.4 + - - +
151B VAL* 4.0 1.3 - - - +
152B TYR* 3.0 53.5 + + - +
153B ALA 3.9 0.3 + - - -
177B ASN 5.9 0.4 - - - -
180B ILE* 3.4 20.2 - - + +
181B VAL* 4.0 23.1 - - + -
184B SER* 2.9 25.9 + - - -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO 3.4 20.2 - - - +
51B TYR* 4.2 3.1 - - + -
56B TYR* 3.3 25.8 - - - +
145B ALA 2.9 17.1 + - - +
146B ARG 3.8 4.0 - - - +
147B LEU 3.1 0.2 - - - -
148B TRP* 1.3 76.7 - - - +
150B HIS* 1.3 59.4 + - - +
153B ALA* 3.0 9.6 + - + +
154B GLY 2.8 24.9 + - - -
155B ALA* 3.0 16.8 + - + -
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.5 28.6 + - + -
23A SER* 4.5 1.8 - - - -
25A ASN* 3.4 19.2 + - - -
28A LYS* 4.9 1.6 + - - -
146B ARG 3.2 12.2 + - - +
147B LEU* 3.2 8.8 + - + +
149B ALA* 1.3 79.2 - - - +
151B VAL* 1.3 75.7 + - + +
154B GLY* 3.6 11.8 + - - -
155B ALA* 2.9 27.8 - - - +
156B PRO 3.2 15.3 - - - +
157B VAL* 3.3 45.3 - - + +
158B SER 4.6 3.3 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.1 20.0 + - - -
30A ASP* 5.3 1.2 - - - +
147B LEU* 3.0 33.0 + - + +
148B TRP* 4.3 2.7 - - - +
150B HIS* 1.3 91.7 - - + +
152B TYR* 1.3 87.7 + - + +
163B THR* 6.2 1.3 - - + -
166B ILE* 5.6 2.9 - - + -
176B ARG* 2.8 35.6 + - - +
180B ILE* 4.1 9.9 - - + -
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.8 12.6 + - - +
30A ASP* 4.7 11.9 - - - -
55B ARG 4.8 0.2 - - - +
77B THR* 3.2 18.2 - - + +
78B LYS* 3.4 55.5 - - + +
148B TRP* 3.0 46.5 + + - +
151B VAL* 1.3 99.9 - - + +
153B ALA* 1.3 60.6 + - - +
154B GLY 3.7 0.9 - - - -
176B ARG* 4.5 3.6 - - - -
177B ASN* 2.6 40.3 + - - +
180B ILE* 3.4 20.8 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 5.3 0.7 - - - -
55A ARG* 2.7 28.6 + - - -
54B GLY* 3.2 11.0 - - - -
55B ARG 3.0 23.3 + - - +
56B TYR* 3.3 44.0 - - + +
148B TRP 3.9 0.2 + - - -
149B ALA* 3.0 15.0 + - - +
152B TYR* 1.3 77.6 - - - +
154B GLY* 1.3 51.2 - - - +
155B ALA 3.5 0.2 - - - -
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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