Contacts of the strand formed by residues 177 - 186 (chain Y) in PDB entry 1I9R
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 TYR 177 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107Y LYS* 3.4 19.2 + - - -
109Y GLU* 3.0 34.5 + - - +
142Y ASN* 2.8 10.9 - - - -
143Y PHE* 2.4 61.6 + - + +
144Y TYR* 4.0 9.9 - + - -
145Y PRO 3.9 3.8 - - - -
146Y ARG* 3.2 51.7 - - + +
167Y VAL* 4.2 4.0 - - + -
168Y THR* 3.1 29.8 - - - -
169Y GLU 4.1 0.2 - - - -
170Y GLN* 3.1 36.4 - - + +
176Y THR* 1.3 71.2 - - - +
178Y SER* 1.3 61.9 + - - +
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Residues in contact with SER 178 (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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169X HIS* 3.4 20.8 - - - -
171X PHE* 3.1 19.7 - - - -
140Y LEU 3.2 10.1 - - - -
141Y ASN* 2.6 33.0 + - - -
142Y ASN* 2.9 1.4 + - - -
143Y PHE* 3.3 1.8 - - - -
167Y VAL* 4.4 0.2 - - - -
168Y THR* 3.0 30.6 + - - -
177Y TYR* 1.3 82.5 + - - +
179Y LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 179 (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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171X PHE* 3.2 10.8 - - - -
139Y LEU* 3.7 1.6 - - - +
140Y LEU* 3.2 36.1 + - + -
143Y PHE* 3.1 20.8 - - + -
146Y ARG* 5.0 3.1 - - - +
148Y ALA* 4.1 17.7 - - + +
150Y VAL* 3.8 15.9 - - + -
165Y GLU* 3.4 30.7 - - + +
166Y SER 3.2 10.5 - - - +
167Y VAL* 3.8 17.0 - - + -
178Y SER* 1.3 72.3 - - - +
180Y SER* 1.3 79.1 + - - +
181Y SER* 3.3 27.4 - - - +
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Residues in contact with SER 180 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171X PHE* 3.4 39.4 - - - +
184X SER* 5.1 6.6 + - - -
137Y VAL* 5.0 8.7 - - - -
138Y CYS 3.7 9.0 - - - -
139Y LEU* 5.0 1.8 - - - -
164Y GLN 3.3 12.8 - - - +
165Y GLU 3.7 0.2 - - - -
166Y SER* 2.7 27.4 + - - -
179Y LEU* 1.3 79.5 - - - +
181Y SER* 1.3 60.9 + - - +
182Y THR* 3.6 6.1 + - - -
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Residues in contact with SER 181 (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 VAL* 3.8 0.3 - - - -
138Y CYS* 2.9 33.9 + - - -
150Y VAL* 4.1 24.9 + - - -
152Y TRP* 2.7 36.9 + - - -
163Y SER* 4.3 5.7 + - - -
164Y GLN 3.6 4.2 + - - -
165Y GLU* 4.1 19.8 - - - +
179Y LEU* 3.3 7.0 - - - +
180Y SER* 1.3 71.7 - - - +
182Y THR* 1.3 59.9 + - - +
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Residues in contact with THR 182 (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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146X LEU* 5.0 5.2 - - + -
182X SER* 6.1 1.1 - - - +
184X SER* 5.7 2.9 - - - -
135Y SER* 4.2 14.1 - - - -
136Y VAL 3.5 2.0 - - - +
137Y VAL* 3.3 31.4 - - + +
152Y TRP* 4.4 0.4 - - - -
163Y SER* 3.8 1.2 - - - -
164Y GLN* 2.8 36.2 + - - +
180Y SER* 3.9 8.7 + - - -
181Y SER* 1.3 76.5 + - - +
183Y LEU* 1.3 70.2 + - - +
184Y THR* 3.6 7.9 + - - +
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Residues in contact with LEU 183 (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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135Y SER* 3.3 3.8 - - - -
136Y VAL* 2.7 58.0 + - + -
152Y TRP* 3.4 37.1 - - + +
154Y VAL* 4.2 9.9 - - + -
159Y GLN* 3.2 43.1 - - + +
162Y ASN 4.3 9.2 - - - +
163Y SER* 4.2 6.3 - - - -
182Y THR* 1.3 74.4 - - - +
184Y THR* 1.3 62.3 + - - +
185Y LEU* 3.6 32.1 - - + -
196Y TYR* 4.2 4.5 - - + -
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Residues in contact with THR 184 (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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148X LYS* 5.1 5.4 - - - -
133Y THR* 4.8 8.7 - - - +
134Y ALA 3.7 5.3 + - - -
135Y SER* 3.4 18.5 - - - +
162Y ASN* 4.0 22.7 + - + +
163Y SER* 5.6 0.7 - - - -
182Y THR* 4.2 8.1 - - - +
183Y LEU* 1.3 81.5 - - - +
185Y LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 185 (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 THR* 4.2 6.9 - - - +
134Y ALA* 2.6 40.1 + - - +
135Y SER* 4.5 0.2 - - - +
136Y VAL* 5.9 0.2 - - + -
154Y VAL* 4.4 9.4 - - + -
159Y GLN* 3.9 21.5 - - - +
162Y ASN 5.6 1.1 - - - +
183Y LEU* 3.6 15.9 - - + +
184Y THR* 1.3 80.0 + - - +
186Y SER* 1.3 61.6 + - - +
189Y ASP* 4.0 14.4 - - + +
190Y TYR* 4.0 19.7 - - + +
192Y LYS* 5.0 4.5 - - - -
196Y TYR* 3.2 40.8 - - + +
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Residues in contact with SER 186 (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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132Y GLY 4.0 5.8 - - - -
133Y THR* 5.0 2.9 - - - +
134Y ALA 4.4 0.2 - - - -
185Y LEU* 1.3 74.1 - - - +
187Y LYS* 1.3 55.8 + - - +
188Y ALA* 2.5 25.1 + - - +
189Y ASP* 2.6 45.7 + - - +
190Y TYR* 2.7 8.2 + - - -
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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