Contacts of the strand formed by residues 173 - 181 (chain I) in PDB entry 4R2G
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 173 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I GLU* 4.5 6.4 + - - -
139I ASP 3.3 13.7 + - - -
140I PHE* 2.6 44.0 + - + +
141I TYR* 3.7 28.6 + + - -
142I PRO 4.0 0.7 - - - -
143I GLY* 3.3 42.2 - - - -
165I PRO* 4.1 6.1 - - + -
166I SER* 3.4 14.1 - - - -
167I LYS* 3.3 52.5 - - + +
168I GLN* 4.7 0.5 - - - +
172I LYS* 1.3 76.0 - - - +
174I ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ILE 3.4 12.1 - - - +
138I SER* 4.8 1.3 - - - -
139I ASP 5.3 0.2 - - - +
140I PHE* 3.4 4.4 - - - -
163I THR* 4.5 2.3 + - - -
164I THR 5.0 0.3 - - - +
165I PRO* 3.7 2.5 - - - +
166I SER* 3.3 20.9 + - - +
168I GLN* 3.4 32.3 - - + +
173I TYR* 1.3 80.8 - - - +
175I ALA* 1.3 62.3 + - - +
182J HIS* 4.0 12.8 - - + -
184J PHE* 4.6 1.6 - - + -
185J PRO* 4.3 17.2 - - + +
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Residues in contact with ALA 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ILE* 2.7 51.1 + - + +
140I PHE* 3.7 4.4 - - + -
145I VAL* 4.1 25.4 - - + -
162I THR* 5.2 3.8 - - + -
163I THR* 3.7 14.4 - - - +
165I PRO* 4.5 10.5 - - + -
174I ALA* 1.3 75.0 - - - +
176I SER* 1.3 64.9 + - - +
184J PHE* 3.7 5.6 - - - -
185J PRO* 5.9 0.4 - - - -
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Residues in contact with SER 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I CYS 3.5 4.7 - - - -
136I LEU* 3.7 7.3 - - - +
137I ILE* 5.4 0.9 - - - -
162I THR* 3.5 4.9 - - - +
163I THR* 2.9 39.0 + - - +
175I ALA* 1.3 72.7 - - - +
177I SER* 1.3 59.8 + - - +
178I TYR* 3.3 30.0 + - - -
184J PHE* 3.4 31.4 - - - +
185J PRO* 3.6 9.0 + - - +
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Residues in contact with SER 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I LEU 3.9 0.2 - - - +
134I VAL* 3.9 0.5 - - - -
135I CYS* 2.9 41.2 + - - -
136I LEU* 5.0 0.2 - - - +
137I ILE* 5.2 1.1 - - - -
147I VAL* 3.3 22.3 - - - +
149I TRP* 2.9 35.8 + - - -
160I VAL* 4.0 0.7 - - - +
162I THR* 3.0 25.6 + - - +
176I SER* 1.3 74.5 - - - +
178I TYR* 1.3 61.4 + - - +
179I LEU 3.8 0.2 + - - -
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Residues in contact with TYR 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I THR* 5.8 5.2 - - - -
133I LEU 3.4 6.1 - - - +
134I VAL* 3.8 23.1 - - + -
149I TRP* 4.4 2.2 - - - -
159I GLY 3.6 3.6 - - - +
161I GLU* 3.3 42.0 + - + +
163I THR* 4.4 0.4 - - + -
176I SER* 3.3 34.2 + - - -
177I SER* 1.3 74.6 + - - +
179I LEU* 1.3 61.1 + - - +
180I SER* 3.8 4.8 + - - -
159J LEU* 3.7 15.0 - - + -
185J PRO 4.5 2.4 + - - -
187J VAL* 3.4 32.3 - - + -
189J GLN* 6.1 1.6 - - - +
195J SER* 3.3 20.2 + - - -
196J LEU* 3.4 2.4 - - - -
197J SER* 3.1 38.5 + - - -
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I THR* 3.3 1.9 - - - -
133I LEU* 2.5 59.2 + - + +
149I TRP* 3.6 47.2 - - + +
156I VAL* 3.9 30.3 - - + -
158I ALA 3.9 5.8 - - - +
159I GLY 3.9 9.2 - - - +
160I VAL* 4.2 7.6 - - + +
178I TYR* 1.3 70.8 - - - +
180I SER* 1.3 69.0 + - - +
181I LEU* 4.1 11.4 - - + -
192I TYR* 3.7 23.8 - - + -
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Residues in contact with SER 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I ALA 3.5 4.7 + - - -
132I THR* 3.2 25.7 - - - +
158I ALA 4.9 0.5 - - - +
159I GLY* 3.1 29.8 + - - +
178I TYR* 4.7 5.2 - - - -
179I LEU* 1.3 78.2 - - - +
181I LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I LYS* 4.8 1.2 - - - +
131I ALA* 2.7 40.0 + - + +
133I LEU* 4.3 13.0 - - + -
179I LEU* 4.1 17.3 - - + -
180I SER* 1.3 77.2 + - - +
182I THR* 1.3 77.4 + - - +
185I GLN* 3.3 17.3 - - + +
186I TRP* 3.6 23.6 - - + +
192I TYR* 3.2 44.6 - - + +
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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