Contacts of the strand formed by residues 173 - 182 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O THR* 5.4 0.2 - - - +
103O LYS* 4.0 20.3 + - - -
105O GLU* 2.9 39.2 + - - +
138O ASN* 3.2 2.3 + - - -
139O PHE* 2.7 58.1 + - + +
140O TYR* 3.3 27.1 - + - -
141O PRO 4.3 7.6 - - - -
142O ARG* 4.0 34.5 - - + +
163O VAL* 4.3 11.2 - - + -
164O THR* 3.8 21.8 - - - +
165O GLU* 4.6 0.4 - - - -
166O GLN* 3.9 23.8 - - + -
172O THR* 1.3 76.3 - - - +
174O SER* 1.3 66.0 + - - +
170P HIS* 5.9 1.1 - - - -
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Residues in contact with SER 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O LEU 3.5 8.5 - - - -
137O ASN* 3.5 3.8 + - - -
138O ASN* 2.9 24.1 + - - -
139O PHE* 3.9 1.1 - - - -
163O VAL* 3.5 4.1 - - - +
164O THR* 3.0 37.0 + - - -
173O TYR* 1.3 73.4 + - - +
175O LEU* 1.3 60.3 + - - +
170P HIS* 3.2 37.6 + - - -
172P PHE* 3.3 15.0 - - - -
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Residues in contact with LEU 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O CYS 3.5 1.0 - - - +
135O LEU* 3.6 4.3 - - - +
136O LEU* 2.7 52.1 + - + +
139O PHE* 3.9 23.1 - - + -
142O ARG* 5.3 3.8 - - - +
144O ALA* 4.6 18.4 - - + +
146O VAL* 4.8 4.3 - - + -
161O GLU* 3.8 28.5 - - + +
162O SER 3.3 9.4 - - - +
163O VAL* 4.4 19.3 - - + -
174O SER* 1.3 76.2 - - - +
176O SER* 1.3 92.2 + - - +
177O SER* 3.9 6.7 - - - +
172P PHE* 3.7 3.6 - - - -
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Residues in contact with SER 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133O VAL* 5.1 5.2 - - - -
134O CYS 3.2 7.0 - - - -
135O LEU* 4.8 3.6 - - - +
160O GLN 5.1 0.2 + - - -
161O GLU* 2.9 7.1 - - - +
162O SER* 2.8 41.4 + - - -
175O LEU* 1.3 77.6 - - - +
177O SER* 1.3 57.4 + - - +
178O THR* 4.2 10.1 + - - -
172P PHE* 3.5 27.1 - - - +
185P SER* 4.5 12.7 + - - -
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Residues in contact with SER 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O VAL 3.6 0.9 - - - +
133O VAL* 3.3 5.0 - - - +
134O CYS* 2.8 44.0 + - - -
146O VAL* 3.7 28.4 - - - +
148O TRP* 3.0 29.0 + - - -
159O SER* 4.1 7.8 + - - -
160O GLN 3.6 3.5 + - - -
161O GLU* 4.2 3.6 - - - +
175O LEU* 3.9 3.5 - - - +
176O SER* 1.3 72.8 - - - +
178O THR* 1.3 65.2 + - - +
179O LEU 4.2 0.2 - - - -
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Residues in contact with THR 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O SER* 3.8 23.1 - - - +
132O VAL 3.4 6.5 - - - +
133O VAL* 3.8 18.1 - - + +
158O ASN 3.9 0.7 - - - +
159O SER* 3.0 24.6 - - - -
160O GLN* 2.7 23.3 + - - +
176O SER* 4.2 9.7 + - - -
177O SER* 1.3 79.0 + - - +
179O LEU* 1.3 62.5 + - - +
180O THR* 4.0 7.9 + - - +
147P LEU* 5.3 7.3 - - + +
149P LYS* 6.4 0.2 - - - -
185P SER* 4.7 4.9 + - - -
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Residues in contact with LEU 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O ALA 3.7 0.9 - - - +
131O SER* 3.3 10.2 + - - -
132O VAL* 2.8 60.7 + - + +
148O TRP* 4.1 43.0 - - + -
150O VAL* 4.2 20.4 - - + -
155O GLN* 4.4 6.1 - - + -
158O ASN* 3.6 37.2 - - - +
159O SER* 4.3 2.5 - - - +
177O SER 4.1 0.4 + - - -
178O THR* 1.3 71.4 - - - +
180O THR* 1.3 60.9 + - - +
181O LEU* 4.1 17.0 - - + -
192O TYR* 4.6 3.8 - - + -
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Residues in contact with THR 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O THR* 4.6 18.6 - - + -
130O ALA 3.8 1.8 - - - -
131O SER* 4.4 9.1 + - - +
158O ASN* 3.0 33.2 + - - +
160O GLN* 5.6 4.2 - - - +
178O THR* 4.1 9.5 + - - +
179O LEU* 1.3 76.9 + - - +
181O LEU* 1.3 65.2 + - - +
149P LYS* 4.9 9.5 - - - +
177P GLN* 6.1 0.9 - - - +
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Residues in contact with LEU 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O THR* 3.6 6.9 - - - +
130O ALA* 2.7 42.2 + - + +
132O VAL* 5.1 3.1 - - + -
150O VAL* 5.2 5.6 - - + -
155O GLN* 5.4 4.3 - - - +
158O ASN* 4.4 13.5 - - - +
179O LEU* 4.1 17.5 - - + -
180O THR* 1.3 79.5 - - - +
182O SER* 1.3 60.3 + - - +
185O ASP* 3.3 23.1 - - - +
186O TYR* 3.9 20.2 - - + -
189O HIS* 6.3 0.4 - - + -
192O TYR* 3.7 38.1 - - + +
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Residues in contact with SER 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O GLY 3.7 12.1 - - - -
129O THR* 4.4 1.1 - - - +
130O ALA 4.5 0.7 - - - -
181O LEU* 1.3 75.6 - - - +
183O LYS* 1.3 55.5 + - - +
184O ALA 4.5 1.0 + - - -
185O ASP* 2.6 35.9 + - - +
186O TYR* 2.8 36.0 + - - +
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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