Contacts of the strand formed by residues 172 - 181 (chain Y) in PDB entry 3HI6
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 172 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171X HIS* 5.8 1.3 - - - -
83Y PHE* 5.6 0.8 - + - -
104Y GLU* 2.9 29.0 + - - +
137Y ASN* 3.0 8.2 + - - -
138Y PHE* 2.8 56.6 + - + +
139Y TYR* 3.6 24.9 - + - -
141Y ARG* 3.6 52.7 - - + +
162Y VAL* 4.2 6.7 - - + -
163Y THR* 3.6 21.8 - - - -
164Y GLU* 4.9 0.7 - - - -
165Y GLN* 3.6 38.5 + - + -
171Y THR* 1.3 74.4 - - - +
173Y SER* 1.3 61.5 + - - +
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Residues in contact with SER 173 (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 HIS* 3.4 17.2 + - - -
173X PHE* 3.5 18.2 - - - -
134Y LEU* 4.7 0.4 - - - -
135Y LEU 3.3 10.5 - - - -
136Y ASN* 2.8 25.0 + - - -
137Y ASN* 3.2 10.2 + - - -
138Y PHE* 3.8 2.2 - - - -
162Y VAL* 3.1 8.3 - - - +
163Y THR* 2.9 40.0 + - - -
172Y TYR* 1.3 72.4 + - - +
174Y LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 174 (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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173X PHE* 3.5 4.7 - - - -
134Y LEU* 3.5 5.2 - - - +
135Y LEU* 2.8 59.1 + - + +
138Y PHE* 3.7 23.1 - - + -
141Y ARG 5.0 3.6 - - - +
143Y ALA* 4.6 11.9 - - + +
145Y VAL* 4.2 11.0 - - + -
160Y GLU* 3.5 25.6 - - + +
161Y SER 3.3 11.7 - - - +
162Y VAL* 4.2 15.0 - - + -
173Y SER* 1.3 76.8 - - - +
175Y SER* 1.3 78.9 + - - +
176Y SER* 3.7 5.2 - - - +
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Residues in contact with SER 175 (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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173X PHE* 3.5 25.3 - - - +
186X SER* 5.0 6.9 + - - -
132Y VAL* 4.5 14.4 - - - -
133Y CYS 3.3 7.2 - - - -
134Y LEU* 4.7 1.3 - - - +
159Y GLN 3.8 0.5 + - - +
160Y GLU* 3.2 4.2 - - - -
161Y SER* 2.8 49.9 + - - -
174Y LEU* 1.3 79.3 - - - +
176Y SER* 1.3 58.7 + - - +
177Y THR* 4.5 7.4 + - - -
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Residues in contact with SER 176 (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 VAL* 3.6 0.8 - - - -
133Y CYS* 2.8 39.1 + - - -
145Y VAL* 3.8 23.7 + - - +
147Y TRP* 3.0 30.6 + - - -
158Y SER* 4.2 7.1 + - - -
159Y GLN 3.4 5.5 + - - -
160Y GLU* 4.0 16.9 + - - +
174Y LEU* 3.7 4.7 - - - +
175Y SER* 1.3 73.0 - - - +
177Y THR* 1.3 61.4 + - - +
178Y LEU 4.0 0.2 - - - -
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Residues in contact with THR 177 (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 LEU* 5.1 8.5 - - + +
186X SER* 4.9 4.7 + - - -
130Y SER* 3.9 29.2 - - - +
131Y VAL 3.5 6.5 - - - +
132Y VAL* 4.1 18.8 - - + +
147Y TRP* 4.5 0.7 - - - -
157Y ASN 3.9 0.2 - - - +
158Y SER* 3.2 3.7 - - - -
159Y GLN* 2.8 42.8 + - - +
175Y SER* 4.5 8.3 + - - -
176Y SER* 1.3 76.1 + - - +
178Y LEU* 1.3 61.7 + - - +
179Y THR* 3.9 12.3 + - - +
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Residues in contact with LEU 178 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129Y ALA 3.6 1.6 - - - +
130Y SER* 3.3 4.0 - - - -
131Y VAL* 2.8 41.7 + - + +
147Y TRP* 3.6 50.0 - - + -
149Y VAL* 4.3 9.2 - - + -
154Y GLN* 4.3 14.4 - - + -
157Y ASN* 3.2 47.3 - - - +
158Y SER* 4.3 2.7 - - - +
176Y SER 3.9 0.8 + - - -
177Y THR* 1.3 71.9 - - - +
179Y THR* 1.3 59.4 + - - +
180Y LEU* 4.0 23.7 + - + -
191Y TYR* 4.7 6.1 - - + -
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Residues in contact with THR 179 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150X LYS* 4.8 15.1 - - - +
178X GLN* 5.5 2.9 + - - +
128Y THR* 6.4 1.3 - - + -
129Y ALA 3.5 9.6 - - - +
130Y SER* 4.2 9.4 + - - +
157Y ASN* 3.0 24.3 + - - +
159Y GLN* 5.6 2.9 + - - +
177Y THR* 4.2 15.8 + - - +
178Y LEU* 1.3 72.5 - - - +
180Y LEU* 1.3 76.0 + - - +
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Residues in contact with LEU 180 (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 THR* 4.2 1.0 - - - -
129Y ALA* 2.9 38.9 + - + +
131Y VAL* 5.3 3.4 - - + -
149Y VAL* 4.8 6.3 - - + -
154Y GLN* 4.4 3.6 - - - +
157Y ASN* 3.2 31.6 - - - +
178Y LEU* 4.1 20.6 - - + +
179Y THR* 1.3 82.6 - - - +
181Y SER* 1.3 68.0 + - - +
184Y ASP* 4.3 16.6 - - + +
185Y TYR* 4.6 9.0 - - + +
188Y HIS* 6.4 0.9 - - + -
191Y TYR* 3.8 33.0 - - + +
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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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127Y GLY 3.9 11.0 - - - -
129Y ALA* 4.6 0.2 - - - -
180Y LEU* 1.3 76.0 - - - +
182Y LYS* 1.3 66.2 + - - +
183Y ALA* 3.7 9.4 + - - +
184Y ASP* 3.0 33.9 + - - +
185Y TYR* 2.9 22.0 + - - +
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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