Contacts of the helix formed by residues 135 - 146 (chain Y) in PDB entry 5A0Q
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 135 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3Y TYR* 3.5 19.4 - - - +
133Y GLY* 3.5 0.4 - - - -
134Y TYR* 1.3 76.9 - - - +
136Y ALA* 1.4 53.5 + - - +
137Y PHE 3.3 0.9 - - - -
138Y LEU* 3.3 9.0 + - - +
139Y THR* 2.8 34.5 + - - +
167Y LEU* 4.1 14.5 - - - +
171Y PHE* 4.2 17.0 - - - -
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Residues in contact with ALA 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X GLN* 4.3 1.1 + - - +
3Y TYR* 3.6 7.0 - - - -
131Y ALA* 4.1 8.3 - - + +
132Y HIS* 3.8 24.0 - - - +
133Y GLY 3.7 18.2 - - - +
135Y GLY* 1.4 75.1 - - - +
137Y PHE* 1.4 68.9 + - + +
138Y LEU 3.2 1.0 + - - -
139Y THR* 3.5 7.6 - - - -
140Y LEU* 3.3 36.1 + - + +
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Residues in contact with PHE 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ILE* 3.8 26.0 - - + -
130L SER 6.1 0.7 - - - -
133L VAL* 3.4 27.3 - - + +
134L TYR* 3.2 36.9 - - - -
29X ILE* 5.3 7.9 - - + -
30X GLN* 4.0 28.9 - - + -
32X GLN* 3.1 32.8 - - + -
133Y GLY 5.6 1.8 - - - -
134Y TYR* 3.6 8.4 + + - +
135Y GLY 3.3 1.0 - - - -
136Y ALA* 1.4 81.3 - - + +
138Y LEU* 1.3 57.1 + - - +
140Y LEU 4.8 0.8 + - - -
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Residues in contact with LEU 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ILE* 3.9 10.8 - - + -
26K VAL* 3.3 36.3 - - + -
133L VAL* 3.4 39.0 - - + +
136L TYR* 5.1 2.2 - - + -
137L GLY* 4.2 4.3 - - - -
135Y GLY* 3.3 10.9 + - - +
136Y ALA 3.2 0.2 - - - -
137Y PHE* 1.3 78.9 - - - +
139Y THR* 1.3 58.8 + - - +
140Y LEU 3.5 0.7 - - - -
141Y SER* 2.9 23.4 + - - -
142Y ILE* 4.1 5.9 - - - +
166Y GLU* 3.5 27.1 - - + +
167Y LEU* 5.4 0.9 - - + -
171Y PHE* 3.6 38.1 - - + +
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Residues in contact with THR 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Y TYR* 2.7 40.6 + - + +
5Y ILE* 5.3 0.7 - - - -
131Y ALA* 4.1 2.6 - - - +
135Y GLY 2.8 19.4 + - - +
136Y ALA* 3.5 4.5 - - - -
138Y LEU* 1.3 71.8 - - - +
140Y LEU* 1.3 65.0 + - - +
141Y SER 3.2 3.1 - - - -
142Y ILE* 3.1 20.9 + - + +
143Y LEU* 3.3 12.7 + - - +
163Y CYS* 3.9 27.1 - - + +
166Y GLU* 3.9 15.7 - - + -
167Y LEU* 4.1 7.2 - - + -
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Residues in contact with LEU 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L TYR* 5.7 0.7 - - + -
166L ARG* 3.8 25.0 + - + +
32X GLN* 3.3 31.0 - - - +
34X VAL* 6.4 0.4 - - - -
117Y TYR* 6.3 1.6 - - + -
129Y PHE* 4.2 12.8 - - + +
130Y ALA* 4.1 12.8 - - - +
131Y ALA* 3.9 38.1 - - + +
136Y ALA* 3.3 22.7 + - + +
137Y PHE 4.8 1.1 - - - +
138Y LEU 3.5 0.8 - - - -
139Y THR* 1.3 79.4 + - - +
141Y SER* 1.3 55.5 + - - +
143Y LEU* 3.7 6.1 + - + -
144Y ASP* 2.9 30.8 + - - +
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Residues in contact with SER 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L TYR* 2.8 49.1 + - - -
137L GLY* 4.0 6.1 - - - -
138L VAL* 3.8 9.3 - - - +
162L GLN* 3.5 13.2 + - - +
166L ARG* 6.0 3.1 - - - +
138Y LEU 2.9 20.2 + - - -
140Y LEU* 1.3 77.0 - - - +
142Y ILE* 1.3 62.0 + - - +
144Y ASP* 4.2 4.9 - - - -
145Y ARG* 3.1 24.4 + - - +
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Residues in contact with ILE 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L GLY* 3.4 28.7 - - - +
138L VAL* 5.0 1.1 - - - -
141L ARG* 3.4 38.6 - - - +
138Y LEU 4.1 0.2 - - - +
139Y THR* 3.1 14.5 + - - +
141Y SER* 1.3 75.1 + - - +
143Y LEU* 1.3 59.8 + - - +
145Y ARG* 3.3 1.4 + - - -
146Y TYR* 2.9 62.6 + - + +
159Y LEU* 5.6 1.6 - - + +
162Y LYS* 5.0 5.6 - - + -
163Y CYS* 4.1 21.3 - - - -
166Y GLU* 3.7 25.1 - - + -
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Residues in contact with LEU 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y ILE* 3.3 32.3 - - + -
6Y GLY 3.7 5.4 - - - +
7Y ILE* 3.8 13.2 - - + -
129Y PHE* 3.6 33.8 - - + -
130Y ALA 4.5 1.1 - - - +
139Y THR 3.3 11.5 + - - +
140Y LEU* 4.0 7.4 - - + +
142Y ILE* 1.3 80.4 - - - +
144Y ASP* 1.3 60.3 + - - +
146Y TYR* 4.7 1.6 - - - +
147Y TYR* 3.1 39.9 + - + +
159Y LEU* 3.8 36.3 - - + -
163Y CYS* 4.3 10.3 - - - -
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Residues in contact with ASP 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L GLN* 2.8 27.1 + - - +
165L TYR* 3.0 43.0 + - - -
166L ARG* 3.9 10.5 - - + +
129Y PHE* 3.4 25.3 - - + -
140Y LEU 2.9 20.6 + - - +
141Y SER* 3.9 2.9 - - - +
142Y ILE 3.3 0.2 - - - -
143Y LEU* 1.3 77.0 - - - +
145Y ARG* 1.3 62.0 + - - +
147Y TYR 4.2 7.3 - - - +
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Residues in contact with ARG 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L VAL* 4.3 15.5 - - + -
158L ARG* 3.7 42.7 - - - +
161L TYR* 4.0 18.0 - - - -
162L GLN* 3.4 33.5 + - + +
141Y SER 3.1 18.0 + - - +
142Y ILE* 3.7 3.4 - - - +
144Y ASP* 1.3 77.9 - - - +
146Y TYR* 1.3 76.2 + - + +
147Y TYR 3.5 3.5 - - - +
148Y THR* 5.8 0.5 - - - +
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Residues in contact with TYR 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L VAL* 5.6 4.3 - - + -
141L ARG* 2.7 43.2 + - + +
142Y ILE* 2.9 47.7 + - + +
145Y ARG* 1.3 92.9 - - + +
147Y TYR* 1.3 64.7 + - - +
148Y THR* 3.6 12.5 + - - +
155Y ARG* 5.7 6.3 - - - -
159Y LEU* 3.7 20.9 - - + -
162Y LYS* 3.6 28.7 + - + -
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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