Contacts of the helix formed by residues 154 - 169 (chain Y) in PDB entry 1T6B
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 LEU 154 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340X LEU* 4.6 19.3 - - + -
341X ALA 4.4 0.2 - - - +
342X GLY 3.6 13.7 - - - +
343X GLU* 4.2 29.2 - - + +
349X THR* 4.7 20.0 - - + +
152Y ASP 3.1 0.4 + - - -
153Y GLY* 1.3 73.7 - - - +
155Y VAL* 1.3 58.3 + - - +
156Y PRO* 3.4 2.5 - - - -
157Y SER* 3.3 19.6 + - - +
158Y TYR* 3.0 50.0 + - + +
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Residues in contact with VAL 155 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341X ALA* 4.0 8.1 - - + -
342X GLY* 3.7 23.1 - - - +
118Y THR 3.4 26.0 - - - +
119Y TYR* 4.3 6.5 - - + -
120Y ILE* 3.8 17.9 - - + -
121Y HIS* 3.6 23.3 - - + +
151Y LEU* 4.0 9.2 - - + -
152Y ASP 3.3 17.5 - - - +
154Y LEU* 1.3 74.6 - - - +
156Y PRO* 1.4 62.3 - - + +
158Y TYR* 3.1 5.1 + - - +
159Y ALA* 2.7 37.6 + - - +
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Residues in contact with PRO 156 (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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151Y LEU* 3.9 22.0 - - + +
152Y ASP 3.2 14.4 - - - +
153Y GLY 3.6 8.5 - - - +
154Y LEU 3.5 3.1 - - - -
155Y VAL* 1.4 90.7 - - + +
157Y SER* 1.3 56.9 + - - +
159Y ALA* 3.7 0.9 - - - +
160Y GLU* 2.7 41.3 + - - +
185Y GLN* 3.4 33.4 - - - +
188Y ARG* 6.1 0.7 - - - +
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Residues in contact with SER 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154Y LEU* 3.3 22.9 + - - +
155Y VAL 3.3 0.6 - - - -
156Y PRO* 1.3 80.5 - - - +
158Y TYR* 1.3 70.3 + - - +
160Y GLU* 3.7 12.0 + - - +
161Y LYS* 3.2 22.9 + - - +
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Residues in contact with TYR 158 (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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342X GLY 3.8 24.2 - - - -
344X ARG* 3.6 33.6 + - + +
348X GLU* 4.1 21.0 + - - +
349X THR* 4.7 3.1 + - - -
121Y HIS* 3.7 31.3 - + + +
154Y LEU* 3.0 44.0 + - + +
155Y VAL* 4.0 1.6 - - - +
157Y SER* 1.3 81.2 + - - +
159Y ALA* 1.3 60.6 + - - +
161Y LYS* 3.5 23.4 + - + +
162Y GLU* 3.0 30.5 + - - +
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Residues in contact with ALA 159 (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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120Y ILE* 3.5 28.5 - - + -
121Y HIS* 3.8 8.8 - - - +
124Y LEU* 3.8 9.2 - - + +
151Y LEU* 4.5 2.2 - - + -
155Y VAL 2.7 22.1 + - - +
156Y PRO 3.7 3.6 - - - +
158Y TYR* 1.3 70.6 - - - +
160Y GLU* 1.3 54.6 + - - +
162Y GLU 3.4 0.3 + - - -
163Y ALA* 2.8 36.3 + - - +
189Y ILE* 3.7 20.3 - - + +
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Residues in contact with GLU 160 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Y PRO* 2.7 33.5 + - - +
157Y SER* 3.7 10.5 - - - +
159Y ALA* 1.3 75.3 - - - +
161Y LYS* 1.3 56.9 + - - +
163Y ALA* 3.4 4.5 - - - +
164Y LYS* 3.1 44.3 + - - +
167Y ARG* 4.5 0.3 + - - -
185Y GLN* 2.9 24.7 + - - -
188Y ARG* 3.3 55.2 + - + +
189Y ILE* 4.8 1.3 - - - +
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Residues in contact with LYS 161 (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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157Y SER 3.2 14.4 + - - +
158Y TYR* 3.7 24.2 - - + +
159Y ALA 3.2 0.2 - - - -
160Y GLU* 1.3 76.0 - - - +
162Y GLU* 1.3 66.0 + - - +
164Y LYS* 3.2 13.5 + - + +
165Y ILE* 3.0 42.6 + - + +
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Residues in contact with GLU 162 (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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121Y HIS* 3.8 8.7 - - + +
124Y LEU* 3.6 15.5 - - + -
125Y LYS* 3.5 52.1 - - - +
128Y ASN* 2.9 36.6 + - - +
158Y TYR 3.0 19.1 + - - +
159Y ALA* 3.9 3.6 - - - +
161Y LYS* 1.3 77.2 - - - +
163Y ALA* 1.3 61.0 + - - +
165Y ILE* 3.1 22.9 + - - +
166Y SER* 3.0 19.3 + - - -
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Residues in contact with ALA 163 (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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124Y LEU* 4.2 6.3 - - + +
159Y ALA 2.8 22.5 + - - +
160Y GLU 3.4 5.2 - - - +
162Y GLU* 1.3 72.1 - - - +
164Y LYS* 1.3 56.9 + - - +
166Y SER* 3.0 27.5 + - - -
167Y ARG* 3.1 22.5 + - - +
173Y VAL* 4.8 3.4 - - + -
189Y ILE* 3.2 42.2 - - + +
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Residues in contact with LYS 164 (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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160Y GLU* 3.1 31.3 + - - +
161Y LYS* 3.2 11.4 + - + +
163Y ALA* 1.3 72.6 - - - +
165Y ILE* 1.3 64.5 + - + +
167Y ARG* 3.5 20.8 + - - +
168Y SER* 3.1 22.7 + - - -
188Y ARG 5.8 1.1 - - - -
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Residues in contact with ILE 165 (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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128Y ASN* 3.5 19.3 - - + +
132Y GLN* 6.1 0.9 - - - +
161Y LYS* 3.0 35.3 + - + +
162Y GLU* 3.1 31.6 + - - +
164Y LYS* 1.3 76.4 - - + +
166Y SER* 1.3 62.3 + - - +
168Y SER* 2.9 26.2 + - - +
169Y LEU* 3.2 19.3 + - + +
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Residues in contact with SER 166 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Y LEU* 4.8 2.8 + - - +
128Y ASN* 2.4 33.1 + - - -
143Y ILE* 3.1 18.1 - - - +
162Y GLU 3.0 8.0 + - - -
163Y ALA* 3.0 12.9 + - - -
165Y ILE* 1.3 78.6 - - - +
167Y ARG* 1.3 58.3 + - - +
169Y LEU* 3.0 21.8 + - - +
171Y ALA* 3.4 21.9 + - - +
173Y VAL* 3.8 18.1 - - - +
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Residues in contact with ARG 167 (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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163Y ALA* 3.1 27.5 + - - +
164Y LYS* 3.5 22.4 - - - +
165Y ILE 3.3 0.2 - - - -
166Y SER* 1.3 75.8 - - - +
168Y SER* 1.3 61.0 + - - +
169Y LEU 3.0 5.9 + - - -
170Y GLY* 3.2 13.2 + - - -
171Y ALA 3.5 16.3 - - - +
173Y VAL* 3.8 11.5 - - + +
188Y ARG 4.5 5.5 + - - -
189Y ILE 2.8 30.5 + - - -
190Y ALA 4.3 4.6 + - - -
191Y ASP* 3.0 44.3 + - - +
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Residues in contact with SER 168 (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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137Y LEU* 4.2 17.0 - - - +
164Y LYS 3.1 15.6 + - - -
165Y ILE* 2.9 19.8 + - - +
167Y ARG* 1.3 75.4 - - - +
169Y LEU* 1.3 65.1 + - - +
170Y GLY 3.4 1.0 + - - -
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Residues in contact with LEU 169 (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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128Y ASN* 3.9 40.8 - - + +
131Y ILE* 4.2 20.7 - - + +
132Y GLN* 4.7 26.2 - - + +
136Y GLY* 3.5 29.8 - - - +
137Y LEU* 4.4 14.1 - - + +
141Y SER* 5.5 0.3 - - - -
165Y ILE* 3.4 22.4 - - + +
166Y SER* 3.0 8.9 + - - +
168Y SER* 1.3 84.5 - - - +
170Y GLY* 1.3 59.9 + - - +
171Y ALA 3.4 1.9 + - - -
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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