Contacts of the strand formed by residues 173 - 182 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E LYS* 5.8 0.2 + - - -
105E GLU* 2.8 42.9 + - - +
138E ASN* 3.3 2.0 - - - -
139E PHE* 2.8 59.3 + - + +
140E TYR* 3.9 21.1 - + - -
142E ARG* 3.5 59.9 - - + -
163E VAL* 4.3 7.6 - - + -
164E THR* 3.6 19.3 - - - -
166E GLN* 3.2 31.0 - - + +
172E THR* 1.3 73.6 - - - +
174E SER* 1.3 65.5 + - - +
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Residues in contact with SER 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU 3.3 13.0 - - - -
137E ASN* 3.6 3.9 + - - -
138E ASN* 3.0 23.6 + - - -
139E PHE* 3.4 2.0 - - - -
163E VAL* 3.3 5.3 - - - +
164E THR* 3.1 36.7 + - - -
173E TYR* 1.3 71.6 + - - +
175E LEU* 1.3 61.9 + - - +
170F HIS* 3.5 31.1 + - - -
172F PHE* 3.6 15.1 - - - -
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Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LEU* 3.6 3.1 - - - +
136E LEU* 2.9 58.6 + - + +
139E PHE* 3.4 18.1 - - + -
142E ARG 6.0 1.1 - - - +
144E ALA* 5.2 10.1 - - + +
146E VAL* 4.7 6.7 - - + -
161E GLU* 3.4 33.9 - - + +
162E SER 3.1 10.5 - - - +
163E VAL* 3.8 15.3 - - + -
174E SER* 1.3 75.6 - - - +
176E SER* 1.3 76.3 + - - +
177E SER* 4.0 9.9 - - - +
172F PHE* 3.6 4.5 - - - -
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Residues in contact with SER 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E VAL* 4.8 13.2 - - - -
134E CYS 3.3 7.9 - - - -
135E LEU* 5.2 1.8 - - - -
160E GLN 4.0 0.5 - - - +
161E GLU* 3.3 2.9 - - - -
162E SER* 2.8 41.4 + - - +
175E LEU* 1.3 78.0 - - - +
177E SER* 1.3 60.0 + - - +
178E THR* 4.3 5.8 + - - -
172F PHE* 3.4 37.9 - - - +
185F SER* 4.8 6.7 + - - -
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Residues in contact with SER 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E VAL 3.7 1.0 - - - +
133E VAL* 3.6 3.2 - - - -
134E CYS* 2.9 37.5 + - - -
146E VAL* 3.8 33.7 - - - +
148E TRP* 3.3 27.5 + - - -
159E SER* 4.3 6.6 + - - -
160E GLN 3.5 11.3 + - - -
161E GLU* 4.5 4.0 - - - +
175E LEU* 4.0 4.8 - - - +
176E SER* 1.3 72.4 - - - +
178E THR* 1.3 61.9 + - - +
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Residues in contact with THR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E SER* 4.1 24.7 - - - +
132E VAL 3.2 10.5 - - - +
133E VAL* 4.2 15.1 - - + +
148E TRP* 4.3 0.2 - - - -
159E SER* 3.0 26.5 - - - -
160E GLN* 3.0 17.0 + - - -
176E SER* 4.7 7.1 + - - -
177E SER* 1.3 74.4 + - - +
179E LEU* 1.3 64.6 - - - +
180E THR* 3.7 7.4 + - - +
147F LEU* 5.1 10.2 - - + +
185F SER* 5.7 2.4 - - - -
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Residues in contact with LEU 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA 3.4 2.9 - - - +
131E SER* 3.3 3.6 - - - -
132E VAL* 2.7 51.5 + - + +
148E TRP* 3.8 54.6 - - + +
150E VAL* 4.6 4.7 - - + -
155E GLN* 4.5 7.0 - - + +
158E ASN* 3.4 33.9 - - - +
159E SER* 4.1 2.0 - - - -
178E THR* 1.3 70.8 - - - +
180E THR* 1.3 59.5 + - - +
181E LEU* 3.6 30.3 - - + -
192E TYR* 4.2 13.7 - - + -
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Residues in contact with THR 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E THR* 4.2 21.1 - - + -
130E ALA 3.6 2.7 - - - -
131E SER* 3.7 14.6 + - - +
158E ASN* 2.9 26.2 + - - +
178E THR* 3.7 9.7 + - - +
179E LEU* 1.3 71.4 - - - +
181E LEU* 1.3 76.7 + - - +
149F LYS* 4.7 2.6 - - - -
177F GLN* 4.6 13.8 + - - +
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Residues in contact with LEU 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E THR* 3.5 4.2 - - - +
130E ALA* 2.5 51.4 + - + +
132E VAL* 5.7 2.0 - - + -
150E VAL* 5.0 6.1 - - + -
155E GLN* 5.3 1.3 - - - +
158E ASN* 3.2 26.9 - - + +
179E LEU* 3.6 30.3 - - + +
180E THR* 1.3 81.7 - - - +
182E SER* 1.3 63.3 + - - +
185E ASP* 4.5 26.5 - - + +
186E TYR* 5.0 3.4 - - + +
189E HIS* 6.0 2.0 - - + -
192E TYR* 4.1 21.8 - - + +
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Residues in contact with SER 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLY 4.2 10.1 - - - -
129E THR* 4.4 2.0 - - - +
130E ALA* 4.2 1.3 - - - +
181E LEU* 1.3 79.9 - - - +
183E LYS* 1.3 64.3 + - - +
184E ALA* 3.3 11.4 + - - +
185E ASP* 3.2 28.9 + - - -
186E TYR* 3.4 18.2 + - - +
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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