Contacts of the helix formed by residues 157 - 168 (chain Y) in PDB entry 2Q4G
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 157 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126Y ASP* 2.5 44.9 + - - -
129Y LEU* 3.2 35.7 - - - +
130Y GLN* 5.9 0.2 - - - -
153Y LEU* 3.6 12.2 - - - +
154Y SER 3.4 5.5 + - - -
156Y ALA* 1.3 76.1 - - - +
158Y CYS* 1.3 60.1 + - - +
159Y GLU 3.5 0.7 - - - -
160Y PRO* 3.5 8.1 - - - -
161Y LEU* 3.3 22.9 + - - +
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Residues in contact with CYS 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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154Y SER 3.2 20.6 - - - -
155Y ALA* 2.9 19.2 + - - +
156Y ALA 2.6 8.1 + - - -
157Y SER* 1.3 74.0 - - - +
159Y GLU* 1.3 58.0 + - - -
161Y LEU* 3.9 8.5 - - - +
162Y ALA* 3.1 17.5 + - - +
181Y ILE* 3.3 29.2 - - - -
185Y GLY* 3.7 9.2 - - - +
188Y VAL* 3.1 19.7 - - + +
189Y LEU* 3.4 29.6 - - + +
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Residues in contact with GLU 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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155Y ALA 4.1 1.2 + - - -
156Y ALA 3.2 4.0 + - - +
158Y CYS* 1.3 73.8 - - - +
160Y PRO* 1.3 77.7 - - + +
162Y ALA* 3.0 2.3 + - - +
163Y SER* 2.9 20.2 + - - +
166Y ARG* 2.6 33.3 + - - -
188Y VAL* 3.7 20.4 - - + +
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Residues in contact with PRO 160 (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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129Y LEU* 4.1 12.3 - - + -
130Y GLN* 3.1 37.0 - - + +
133Y CYS* 4.0 10.6 - - + +
156Y ALA 3.0 18.4 - - - +
157Y SER* 3.5 10.3 - - - +
159Y GLU* 1.3 95.4 - - + +
161Y LEU* 1.3 61.1 + - - +
163Y SER* 3.0 25.8 + - - +
164Y VAL* 3.5 8.7 + - - +
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Residues in contact with LEU 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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129Y LEU* 3.8 14.4 - - + -
133Y CYS* 4.1 15.9 - - - -
136Y LEU* 5.1 1.3 - - + -
146Y LEU* 4.3 15.3 - - + -
148Y LEU* 3.9 33.0 - - + -
153Y LEU* 4.4 9.2 - - + -
157Y SER 3.3 20.6 + - - +
158Y CYS* 4.1 8.7 - - - +
159Y GLU 3.2 0.6 - - - -
160Y PRO* 1.3 79.1 - - - +
162Y ALA* 1.3 63.1 + - - +
164Y VAL* 2.9 20.1 + - + +
165Y LEU* 3.3 15.5 + - - +
174Y LEU* 4.7 17.4 - - + +
176Y VAL* 4.6 12.3 - - + -
189Y LEU* 5.3 11.0 - - + -
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Residues in contact with ALA 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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158Y CYS 3.1 17.7 + - - +
159Y GLU* 3.0 22.6 + - - +
161Y LEU* 1.3 77.1 - - - +
163Y SER* 1.3 59.1 + - - +
165Y LEU* 3.6 10.2 + - - +
166Y ARG* 3.4 39.0 + - - +
188Y VAL* 3.8 23.1 - - + +
189Y LEU* 5.0 2.9 - - - +
192Y GLY* 4.5 6.7 - - - -
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Residues in contact with SER 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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137Y LEU* 3.3 31.5 - - - +
159Y GLU* 2.9 21.8 + - - +
160Y PRO* 3.0 17.8 + - - +
162Y ALA* 1.3 78.0 - - - +
164Y VAL* 1.3 60.0 + - - +
166Y ARG* 4.1 11.8 + - - +
167Y ALA* 3.3 15.2 + - - +
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Residues in contact with VAL 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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133Y CYS* 4.2 9.4 - - + -
136Y LEU* 3.8 37.5 - - + -
137Y LEU* 4.0 13.5 - - + -
146Y LEU* 5.9 2.0 - - + -
160Y PRO 3.9 12.1 - - - +
161Y LEU* 2.9 12.1 + - + +
163Y SER* 1.3 76.0 - - - +
165Y LEU* 1.3 63.5 + - + +
166Y ARG 3.1 2.0 - - - -
167Y ALA* 2.9 3.3 + - - -
168Y LYS* 2.7 55.5 + - + +
171Y PHE* 4.6 15.3 - - + -
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Residues in contact with LEU 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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161Y LEU 3.3 10.5 + - - +
162Y ALA* 3.6 10.3 + - - +
164Y VAL* 1.3 79.6 - - + +
166Y ARG* 1.3 58.8 + - - +
168Y LYS* 3.3 12.9 - - - +
171Y PHE* 3.6 36.6 - - + -
174Y LEU* 4.0 27.4 - - + -
189Y LEU* 4.2 11.4 - - + +
192Y GLY 4.1 10.5 - - - +
193Y LEU* 4.1 40.2 - - + +
196Y SER* 2.6 28.1 + - - -
198Y CYS* 4.8 3.1 - - - -
200Y LEU* 4.6 5.6 - - + -
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Residues in contact with ARG 166 (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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159Y GLU* 2.6 35.0 + - - -
162Y ALA* 3.4 22.7 + - - +
163Y SER* 4.1 8.9 + - - +
164Y VAL 3.1 0.4 - - - -
165Y LEU* 1.3 79.8 - - - +
167Y ALA* 1.3 61.4 + - - +
168Y LYS 4.8 0.2 - - - -
169Y PRO* 5.2 1.4 - - - +
188Y VAL 5.5 0.2 + - - -
191Y GLN* 4.7 4.4 - - - +
192Y GLY* 3.7 25.2 - - - +
195Y ASP* 3.4 43.9 + - + +
196Y SER* 4.0 5.8 - - - -
197Y PRO* 4.4 12.8 - - - +
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Residues in contact with ALA 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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137Y LEU* 3.9 21.3 - - + +
163Y SER 3.3 16.6 + - - +
164Y VAL* 2.9 5.6 + - - +
166Y ARG* 1.3 80.2 - - - +
168Y LYS* 1.3 72.2 + - + +
169Y PRO* 2.9 15.6 - - - +
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Residues in contact with LYS 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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136Y LEU 2.6 30.8 + - - -
137Y LEU 4.3 4.2 + - - -
138Y ASP 3.5 10.9 + - - -
139Y PRO* 4.8 3.2 + - - +
141Y CYS* 2.9 34.5 + - - +
142Y ARG* 5.7 1.1 - - - -
143Y LEU 4.6 6.7 - - - +
164Y VAL* 2.7 40.5 + - + +
165Y LEU 3.3 13.8 + - - +
166Y ARG 4.8 0.9 - - - -
167Y ALA* 1.3 82.4 + - - +
169Y PRO* 1.3 65.7 - - + +
170Y ASP 3.2 4.5 + - - +
171Y PHE* 3.6 32.6 + - + +
196Y SER* 3.4 7.4 + - - -
198Y CYS* 3.6 7.4 - - - +
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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