Contacts of the helix formed by residues 134 - 150 (chain Y) in PDB entry 5A31
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 SER 134 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y LYS* 6.2 0.2 - - - +
132Y LEU 3.2 5.2 + - - -
133Y PRO* 1.3 70.5 - - - +
135Y GLU* 1.3 68.4 + - - +
136Y ILE* 3.6 20.1 + - - +
137Y GLU* 2.5 45.7 + - - +
138Y VAL* 3.1 16.0 + - - +
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Residues in contact with GLU 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y TYR* 3.9 9.3 + - - -
104Y LEU* 4.3 15.4 - - + +
107Y LYS* 4.0 35.1 - - + +
108Y LYS* 5.9 6.3 - - - +
133Y PRO 3.5 2.8 + - - -
134Y SER* 1.3 73.7 + - - +
136Y ILE* 1.3 68.5 + - + +
138Y VAL* 3.3 6.0 + - - +
139Y LYS* 3.0 53.3 + - + +
166Y GLN* 5.8 1.1 - - - +
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Residues in contact with ILE 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Y SER* 3.1 15.0 - - - +
135Y GLU* 1.3 92.5 - - + +
137Y GLU* 1.3 57.6 + - + +
139Y LYS* 3.4 7.7 + - + +
140Y TYR* 3.0 27.2 + - - +
162Y ILE* 4.0 28.4 - - + +
166Y GLN* 4.2 31.2 - - + +
167Y ARG* 5.1 0.4 - - - -
168Y THR* 4.2 14.4 - - + +
171Y ILE* 3.6 31.7 - - + +
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Residues in contact with GLU 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Y PRO* 3.4 10.6 - - + +
134Y SER* 2.5 44.4 + - - +
136Y ILE* 1.3 77.3 - - + +
138Y VAL* 1.3 61.2 + - + +
140Y TYR* 3.3 10.6 + - - +
141Y LYS* 3.0 35.3 + - + +
170Y LYS* 5.1 13.5 - - - +
171Y ILE* 5.8 0.7 - - - -
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Residues in contact with VAL 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Y TYR* 3.7 18.8 - - + +
81Y VAL* 4.1 21.8 - - + -
100Y TYR* 3.3 39.1 - - + +
103Y ALA* 4.7 6.1 - - + -
104Y LEU* 3.6 22.0 - - + -
133Y PRO* 4.5 4.5 - - + -
134Y SER 3.1 15.5 + - - +
135Y GLU 3.5 6.1 - - - +
136Y ILE 3.3 0.2 - - - -
137Y GLU* 1.3 76.7 - - + +
139Y LYS* 1.3 57.7 + - - +
141Y LYS* 3.0 10.6 + - - +
142Y LEU* 2.9 25.6 + - - +
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Residues in contact with LYS 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Y LEU* 4.2 24.5 - - + -
108Y LYS* 6.6 0.2 - - - +
135Y GLU* 3.0 42.4 + - + +
136Y ILE* 3.6 7.2 - - + +
138Y VAL* 1.3 72.4 - - - +
140Y TYR* 1.3 65.2 + - - +
142Y LEU* 3.2 11.6 - - - +
143Y ALA* 3.0 22.7 + - - +
158Y ILE* 3.7 36.0 + - + +
159Y LEU* 4.4 2.2 - - + +
161Y GLY* 4.4 6.9 + - - -
162Y ILE* 3.6 40.0 - - + +
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Residues in contact with TYR 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X GLY 5.2 4.7 + - - -
89X HIS* 6.1 1.0 - - - -
136Y ILE 3.0 14.9 + - - +
137Y GLU* 3.3 14.4 - - - +
139Y LYS* 1.3 76.0 - - - +
141Y LYS* 1.3 61.6 + - + +
143Y ALA* 3.1 4.7 + - - +
144Y GLU* 2.9 58.3 + - + +
159Y LEU* 4.3 8.2 - - + +
170Y LYS* 3.7 49.2 + - + +
171Y ILE* 3.9 24.7 - - + -
173Y MET* 5.7 3.8 - - - +
174Y MET* 3.6 34.5 - - + +
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Residues in contact with LYS 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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50Y HIS* 6.2 0.6 - - - -
85Y ASP* 3.6 23.9 + - - +
88Y PHE* 4.4 21.5 - - + -
100Y TYR* 3.5 33.0 - - + +
137Y GLU* 3.0 19.8 + - + +
138Y VAL* 3.0 8.7 + - - +
140Y TYR* 1.3 78.9 - - + +
142Y LEU* 1.3 63.5 + - - +
144Y GLU* 3.2 23.0 + - - +
145Y CYS* 3.1 28.0 + - - -
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Residues in contact with LEU 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y VAL* 3.5 48.0 - - + +
100Y TYR* 3.5 20.5 - - + -
101Y THR* 4.3 9.6 - - + +
104Y LEU* 4.3 19.7 - - + -
138Y VAL 2.9 11.4 + - - +
139Y LYS* 3.2 11.0 - - - +
141Y LYS* 1.3 75.3 - - - +
143Y ALA* 1.3 58.8 + - - +
145Y CYS* 3.1 7.1 + - - +
146Y TYR* 2.9 44.5 + - + +
158Y ILE* 4.0 33.0 - - + -
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Residues in contact with ALA 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139Y LYS 3.0 12.7 + - - +
140Y TYR 3.1 4.9 + - - +
142Y LEU* 1.3 73.8 - - - +
144Y GLU* 1.3 64.1 + - - +
146Y TYR* 3.4 6.7 + - - +
147Y THR* 2.9 29.4 + - - -
155Y ALA* 3.9 16.2 - - + +
158Y ILE* 5.1 2.9 - - + -
159Y LEU* 3.9 21.1 - - + -
174Y MET* 3.4 24.7 - - + -
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Residues in contact with GLU 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89X HIS* 5.7 5.4 - - - -
88Y PHE* 3.6 29.2 - - + -
140Y TYR* 2.9 49.3 + - + +
141Y LYS* 3.2 22.4 + - - +
143Y ALA* 1.3 77.0 - - - +
145Y CYS* 1.3 61.9 + - - +
147Y THR* 3.2 9.9 + - - -
148Y VAL* 3.0 27.9 + - + +
174Y MET* 4.2 17.7 - - - +
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Residues in contact with CYS 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Y PHE* 3.4 31.4 - - - -
93Y TYR* 3.9 21.7 - - + +
96Y ALA* 4.1 17.7 - - - -
97Y VAL* 3.6 19.3 - - + -
100Y TYR* 4.7 4.0 - - - -
141Y LYS 3.1 21.2 + - - -
142Y LEU* 3.1 8.0 + - - +
144Y GLU* 1.3 73.5 - - - +
146Y TYR* 1.3 63.1 + - - +
148Y VAL* 3.2 4.5 + - - +
149Y LEU* 3.0 28.0 + - - +
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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
----------------------------------------------------------
94Y ARG* 5.1 4.3 - - - -
97Y VAL* 3.6 25.8 - - + +
101Y THR* 5.2 1.4 + - - -
142Y LEU* 2.9 46.4 + - + +
143Y ALA* 3.7 7.0 - - - +
144Y GLU 3.3 0.2 - - - -
145Y CYS* 1.3 76.6 - - - +
147Y THR* 1.3 62.1 + - - +
149Y LEU* 3.1 20.2 + - + +
150Y LYS 3.0 17.0 + - - -
151Y GLN* 3.1 27.9 + - + +
154Y ASP* 3.1 48.6 - - + -
155Y ALA* 4.0 7.2 - - + +
158Y ILE* 4.1 18.8 - - + +
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Residues in contact with THR 147 (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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143Y ALA 2.9 15.9 + - - -
144Y GLU* 3.2 11.9 + - - -
146Y TYR* 1.3 74.4 - - - +
148Y VAL* 1.3 60.5 + - + +
150Y LYS* 2.9 23.5 + - - +
151Y GLN 5.1 1.8 - - - +
152Y ASP* 5.0 7.4 - - - +
155Y ALA* 4.1 11.3 - - - +
174Y MET* 4.6 7.5 - - + -
178Y LEU* 4.2 23.5 - - + +
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Residues in contact with VAL 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X LYS* 6.2 2.2 - - - +
88Y PHE* 5.5 2.7 - - + -
93Y TYR* 3.2 53.4 - - + +
144Y GLU* 3.0 20.0 + - + +
145Y CYS 3.7 6.5 - - - +
147Y THR* 1.3 77.4 - - + +
149Y LEU* 1.3 61.0 + - - +
150Y LYS* 3.3 16.8 + - - +
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Residues in contact with LEU 149 (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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334X ILE 5.3 1.3 - - - +
93Y TYR* 3.6 26.9 - - + -
94Y ARG* 3.6 47.6 - - - +
97Y VAL* 4.3 12.6 - - + -
145Y CYS 3.0 21.4 + - - +
146Y TYR* 3.4 26.0 - - + +
147Y THR 3.1 0.2 - - - -
148Y VAL* 1.3 74.6 - - + +
150Y LYS* 1.3 72.5 + - - +
151Y GLN* 3.5 16.2 + - - +
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Residues in contact with LYS 150 (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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146Y TYR 3.0 0.4 + - - -
147Y THR 2.9 16.5 + - - +
148Y VAL 3.9 12.5 + - - +
149Y LEU* 1.3 81.1 - - - +
151Y GLN* 1.3 61.5 + - - +
152Y ASP* 3.4 16.1 + - - +
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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
------------------------------------------------------------
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