Contacts of the strand formed by residues 178 - 187 (chain L) in PDB entry 3IFL
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 178 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110L GLU* 2.7 38.0 + - - +
111L LEU 4.7 0.5 + - - -
143L ASN 3.0 6.3 + - - -
144L PHE* 2.8 59.5 + - + +
145L TYR* 3.8 18.0 - + - -
147L LYS* 3.6 39.8 - - + +
168L TRP* 6.1 2.9 - + + -
169L THR* 4.4 11.7 - - - +
170L ASP* 5.0 1.1 - - - -
171L GLN* 3.3 53.4 + - + -
176L SER 3.8 0.9 - - - -
177L THR* 1.3 75.2 - - - +
179L SER* 1.3 63.9 + - - +
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Residues in contact with SER 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H HIS* 3.3 26.3 + - - -
173H PHE* 3.7 10.3 - - - -
141L LEU 3.4 5.8 - - - -
142L ASN* 3.4 16.9 - - - -
143L ASN* 2.9 21.0 + - - -
144L PHE* 3.7 3.6 - - - -
168L TRP* 3.5 5.2 - - - +
169L THR* 3.1 38.9 + - - +
177L THR* 5.1 0.2 + - - -
178L TYR* 1.3 73.8 + - - +
180L MET* 1.3 65.2 + - - +
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Residues in contact with MET 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H PHE* 3.4 9.5 - - - -
140L PHE* 3.7 1.9 - - - -
141L LEU* 2.8 52.4 + - + +
144L PHE* 4.2 4.9 - - + -
149L ILE* 3.7 24.5 - - - -
151L VAL* 3.7 24.0 - - + -
166L ASN* 3.6 40.8 - - + +
167L SER 3.1 13.0 - - - +
168L TRP* 3.5 29.2 - - + +
179L SER* 1.3 77.5 - - - +
181L SER* 1.3 66.7 + - - +
182L SER* 4.4 1.3 - - - -
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Residues in contact with SER 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H PHE* 3.5 25.3 - - - +
185H SER* 5.3 4.4 + - - -
138L VAL* 5.3 1.3 - - - -
139L CYS 3.4 5.4 - - - -
140L PHE* 4.0 15.5 - - - -
165L LEU 4.6 1.0 + - - -
166L ASN* 3.2 7.1 - - - +
167L SER* 2.8 50.0 + - - +
180L MET* 1.3 78.1 - - - +
182L SER* 1.3 60.0 + - - +
183L THR* 4.7 9.5 + - - -
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Residues in contact with SER 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L CYS* 2.8 36.6 + - - -
141L LEU* 4.4 3.8 - - - +
151L VAL* 3.9 18.6 - - - +
153L TRP* 2.8 33.2 + - - -
164L VAL* 3.5 3.1 - - - +
165L LEU 3.6 0.2 - - - -
166L ASN* 2.7 26.6 + - - +
180L MET* 4.4 4.0 - - - -
181L SER* 1.3 74.2 - - - +
183L THR* 1.3 60.8 + - - +
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Residues in contact with THR 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LEU* 5.1 7.4 - - + +
183H THR* 5.8 4.9 - - + +
185H SER* 4.9 3.8 + - - -
136L SER* 4.3 11.9 - - - -
137L VAL 3.3 9.9 - - - +
138L VAL* 4.0 25.3 - - + +
153L TRP* 4.5 0.9 - - - -
163L GLY 3.2 5.0 - - - +
164L VAL* 3.3 3.0 - - - -
165L LEU* 2.9 40.8 + - - +
181L SER* 4.7 6.9 + - - -
182L SER* 1.3 77.7 + - - +
184L LEU* 1.3 61.2 + - - +
185L THR* 3.8 17.4 + - - +
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Residues in contact with LEU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ALA 3.8 1.4 - - - +
136L SER* 3.5 1.6 - - - -
137L VAL* 2.8 44.6 + - + +
153L TRP* 3.9 36.6 - - + -
155L ILE* 3.9 28.7 - - + -
160L ARG* 3.9 14.6 - - + -
162L ASN 3.6 24.2 - - - +
163L GLY* 3.5 2.5 - - - +
164L VAL* 3.9 11.2 - - + +
183L THR* 1.3 70.7 - - - +
185L THR* 1.3 63.5 + - - +
186L LEU* 3.9 25.5 + - + -
197L TYR* 4.4 7.2 - - + -
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Residues in contact with THR 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LYS* 3.7 12.3 + - - +
178H GLN* 2.8 42.2 + - - +
135L ALA 3.8 3.1 - - - +
136L SER* 4.0 11.4 + - - +
160L ARG* 4.8 1.4 + - - -
163L GLY* 2.9 30.3 + - - +
165L LEU* 5.8 0.2 - - - +
183L THR* 4.0 15.2 + - - +
184L LEU* 1.3 73.8 - - - +
186L LEU* 1.3 75.4 + - - +
190L GLU* 4.7 1.4 - - - +
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Residues in contact with LEU 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L GLY* 4.7 1.2 - - - -
135L ALA* 2.9 30.7 + - + +
137L VAL* 4.6 4.3 - - + -
155L ILE* 4.4 4.9 - - + -
160L ARG* 3.3 37.9 - - - +
184L LEU* 3.9 23.1 - - + +
185L THR* 1.3 84.7 - - - +
187L THR* 1.3 73.4 + - - +
190L GLU* 3.5 14.1 - - + +
191L TYR* 4.2 16.4 - - + +
194L HIS* 6.3 0.9 - - + -
197L TYR* 3.6 35.9 - - + +
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Residues in contact with THR 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L GLY 5.4 0.7 - - - -
134L GLY* 5.4 1.8 - - - -
135L ALA* 4.4 0.9 - - - -
186L LEU* 1.3 77.7 - - - +
188L LYS* 1.3 63.7 + - - +
189L ASP* 3.6 10.1 + - - +
190L GLU* 3.0 39.3 + - - +
191L TYR* 3.0 19.6 + - - +
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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