Contacts of the strand formed by residues 173 - 182 (chain I) in PDB entry 3KYM
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
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Residue Dist Surf HB Arom Phob DC
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103I LYS* 4.2 13.6 + - - -
105I GLU* 2.9 33.9 + - - +
138I ASN* 2.9 11.3 + - - -
139I PHE* 2.9 57.2 + - + +
140I TYR* 3.8 25.4 - + - -
142I ARG* 3.6 47.4 - - + +
163I VAL* 4.5 2.5 - - + -
164I THR* 3.5 24.9 - - - -
165I GLU* 4.4 3.8 - - - -
166I GLN* 3.5 27.3 + - + -
172I THR* 1.3 78.4 - - - +
174I SER* 1.3 62.7 + - - +
170J HIS* 6.2 0.7 - - - -
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Residues in contact with SER 174 (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 LEU* 4.9 0.9 - - - -
136I LEU 3.4 9.4 - - - -
137I ASN* 3.6 4.4 + - - -
138I ASN* 3.1 28.1 + - - -
139I PHE* 3.7 2.2 - - - -
163I VAL* 3.8 4.5 - - - +
164I THR* 2.9 37.8 + - - -
173I TYR* 1.3 73.9 + - - +
175I LEU* 1.3 62.8 + - - +
170J HIS* 3.1 28.9 + - - -
172J PHE* 3.3 14.1 - - - -
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Residues in contact with LEU 175 (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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134I CYS 3.7 0.3 - - - +
135I LEU* 3.3 4.5 - - - +
136I LEU* 2.7 59.6 + - + +
139I PHE* 3.5 24.9 - - + -
142I ARG* 5.3 5.2 - - - +
144I ALA* 4.9 11.0 - - + +
161I GLU* 3.9 27.4 - - + +
162I SER 3.5 10.1 - - - +
163I VAL* 3.8 22.0 - - + -
174I SER* 1.3 76.0 - - - +
176I SER* 1.3 78.7 + - - +
177I SER* 3.8 5.4 - - - +
172J PHE* 3.3 8.4 - - - -
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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
----------------------------------------------------------
133I VAL* 5.0 6.3 - - - -
134I CYS 3.3 9.2 - - - -
135I LEU* 5.1 2.0 - - - -
160I GLN 4.0 0.7 - - - +
161I GLU* 3.3 0.9 - - - -
162I SER* 3.1 30.8 + - - -
175I LEU* 1.3 81.2 - - - +
177I SER* 1.3 58.8 + - - +
178I THR* 4.1 9.8 + - - -
172J PHE* 3.1 36.4 - - - +
185J SER* 4.8 12.0 + - - -
187J VAL* 6.4 0.7 - - - -
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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
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133I VAL* 4.8 0.2 - - - -
134I CYS* 3.1 32.4 + - - -
136I LEU* 6.0 0.2 - - - +
146I VAL* 3.3 28.6 - - - +
148I TRP* 2.7 35.5 + - - -
159I SER* 4.8 3.5 + - - -
160I GLN 3.5 4.6 + - - -
161I GLU* 3.8 14.6 - - - -
175I LEU* 3.8 4.4 - - - +
176I SER* 1.3 75.8 - - - +
178I THR* 1.3 59.8 + - - +
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Residues in contact with THR 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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131I SER* 4.0 17.9 - - - +
132I VAL 3.5 7.9 - - - +
133I VAL* 3.8 16.4 - - + +
159I SER* 3.5 7.5 - - - -
160I GLN* 2.8 37.4 + - - +
176I SER* 4.7 9.9 + - - -
177I SER* 1.3 72.7 + - - +
179I LEU* 1.3 72.0 + - - +
180I THR* 3.9 8.8 + - - +
147J LEU* 5.0 9.5 - - + +
183J SER* 5.9 2.0 - - - +
185J SER* 5.2 2.4 + - - -
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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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130I ALA 3.7 0.2 - - - +
131I SER* 3.3 7.3 - - - -
132I VAL* 2.9 48.9 + - + +
148I TRP* 3.3 49.9 - - + -
150I VAL* 5.0 4.5 - - + -
155I GLN* 4.3 12.8 - - + +
158I ASN* 3.8 34.3 - - - +
159I SER* 4.2 7.8 - - - -
177I SER 3.9 2.4 + - - -
178I THR* 1.3 73.2 - - - +
180I THR* 1.3 60.0 + - - +
181I LEU* 3.9 20.0 - - + -
192I TYR* 4.5 13.0 - - + -
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Residues in contact with THR 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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129I THR* 4.1 18.8 - - + -
130I ALA 3.4 8.1 - - - +
131I SER* 4.2 8.8 + - - +
158I ASN* 3.8 19.5 + - - +
159I SER* 5.7 0.5 - - - -
178I THR* 3.9 11.7 + - - +
179I LEU* 1.3 78.4 + - - +
181I LEU* 1.3 75.4 + - - +
149J LYS* 4.8 6.5 + - - +
177J GLN* 5.6 4.1 + - - +
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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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129I THR* 3.7 6.5 - - - +
130I ALA* 2.8 37.5 + - + +
132I VAL* 5.3 2.7 - - + -
155I GLN* 5.6 3.1 - - - +
158I ASN* 3.7 16.6 - - - +
179I LEU* 3.9 22.9 - - + -
180I THR* 1.3 93.7 - - - +
182I SER* 1.3 63.9 + - - +
185I ASP* 4.6 13.2 - - - +
186I TYR* 4.0 24.9 - - + +
189I HIS* 6.5 0.4 - - + -
192I TYR* 3.9 29.4 - - + +
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Residues in contact with SER 182 (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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128I GLY 4.4 6.5 - - - -
129I THR* 4.8 1.1 - - - +
181I LEU* 1.3 74.6 - - - +
183I LYS* 1.3 56.2 + - - +
184I ALA* 4.4 5.0 - - - +
185I ASP* 2.7 35.4 + - - +
186I TYR* 2.6 34.9 + - - +
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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