Contacts of the strand formed by residues 173 - 182 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G LYS* 5.6 4.9 + - - -
105G GLU* 3.1 31.7 + - - +
138G ASN* 3.1 7.7 + - - -
139G PHE* 2.8 58.0 + - + +
140G TYR* 3.9 20.9 - + - -
142G ARG* 3.6 59.0 + - + +
163G VAL* 4.3 1.1 - - + -
164G THR* 3.3 28.3 - - - +
165G GLU* 4.2 4.5 - - - -
166G GLN* 3.4 28.4 - - + +
172G THR* 1.3 74.4 - - - +
174G SER* 1.3 64.4 + - - +
170H HIS* 5.9 0.7 - - - -
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Residues in contact with SER 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G LEU 3.4 12.8 - - - -
137G ASN* 3.2 23.4 + - - -
138G ASN* 3.2 10.7 + - - -
139G PHE* 3.9 2.9 - - - -
163G VAL* 3.4 6.5 - - - +
164G THR* 2.7 38.2 + - - -
173G TYR* 1.3 72.2 + - - +
175G LEU* 1.3 60.1 + - - +
170H HIS* 3.5 23.9 + - - -
172H PHE* 3.8 17.2 - - - -
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Residues in contact with LEU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G CYS 3.8 0.9 - - - +
135G LEU* 3.7 6.6 - - - +
136G LEU* 3.1 48.6 + - + +
139G PHE* 3.8 24.0 - - + -
142G ARG* 5.1 5.8 - - - +
144G ALA* 5.1 9.6 - - + +
146G VAL* 4.5 2.5 - - + -
161G GLU* 4.0 30.3 - - + +
162G SER 3.3 10.3 - - - +
163G VAL* 4.2 20.4 - - + -
174G SER* 1.3 77.0 - - - +
176G SER* 1.3 77.4 + - - +
177G SER* 4.1 6.3 - - - +
172H PHE* 3.6 4.5 - - - -
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Residues in contact with SER 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G VAL* 5.6 4.9 - - - -
134G CYS 3.6 6.3 - - - -
135G LEU* 5.1 0.9 - - - +
160G GLN 4.7 1.2 + - - -
161G GLU* 2.9 7.3 - - - -
162G SER* 2.7 52.5 + - - -
175G LEU* 1.3 75.3 - - - +
177G SER* 1.3 59.4 + - - +
178G THR* 5.1 6.1 + - - -
172H PHE* 3.5 27.1 - - - +
185H SER* 5.2 8.4 + - - -
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Residues in contact with SER 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G VAL* 3.4 3.1 - - - -
134G CYS* 2.7 52.1 + - - -
136G LEU* 6.5 0.7 - - - -
146G VAL* 4.1 15.1 - - - +
148G TRP* 3.0 27.1 + - - -
159G SER* 4.2 8.0 + - - -
160G GLN 3.4 4.8 + - - -
161G GLU* 4.3 13.6 - - - +
175G LEU* 4.1 5.1 - - - +
176G SER* 1.3 73.7 - - - +
178G THR* 1.3 62.0 + - - +
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Residues in contact with THR 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G SER* 4.3 14.6 - - - +
132G VAL 3.5 7.4 - - - +
133G VAL* 3.0 26.4 - - + +
158G ASN 4.0 1.9 - - - +
159G SER* 3.0 6.1 - - - -
160G GLN* 2.8 43.3 + - - +
176G SER* 5.1 6.0 + - - -
177G SER* 1.3 73.9 + - - +
179G LEU* 1.3 69.4 + - - +
180G THR* 4.2 9.1 + - - +
147H LEU* 5.3 8.8 - - + +
149H LYS* 6.1 1.8 - - + -
183H SER* 5.9 2.7 - - - +
185H SER* 5.8 1.6 - - - -
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Residues in contact with LEU 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ALA 3.9 1.0 - - - +
131G SER* 3.5 5.5 - - - -
132G VAL* 3.0 52.2 + - + +
148G TRP* 3.6 58.3 - - + +
150G VAL* 4.8 5.2 - - + -
155G GLN* 4.3 11.2 - - + -
158G ASN* 3.9 28.7 - - - +
159G SER* 4.3 4.7 - - - +
177G SER 4.2 0.4 - - - -
178G THR* 1.3 73.0 - - - +
180G THR* 1.3 61.4 + - - +
181G LEU* 4.7 13.7 - - + -
192G TYR* 4.5 13.0 - - + -
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Residues in contact with THR 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G THR* 3.5 30.3 - - + -
130G ALA 3.8 3.6 - - - +
131G SER* 4.4 6.2 + - - +
158G ASN* 3.3 41.0 + - - +
178G THR* 4.4 11.1 + - - +
179G LEU* 1.3 76.8 + - - +
181G LEU* 1.3 68.7 + - - +
149H LYS* 5.0 6.6 - - - +
177H GLN* 5.7 2.9 + - - +
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Residues in contact with LEU 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G THR* 3.7 7.2 - - - +
130G ALA 2.9 39.3 + - - +
132G VAL* 4.5 11.4 - - + -
150G VAL* 5.1 5.4 - - + -
155G GLN* 5.0 11.7 - - - +
158G ASN* 4.5 9.2 - - - +
179G LEU* 4.7 15.5 - - + -
180G THR* 1.3 82.8 - - - +
182G SER* 1.3 67.9 + - - +
185G ASP* 4.1 22.9 - - + +
186G TYR* 3.9 32.5 - - + +
189G HIS* 6.1 1.3 - - + -
192G TYR* 4.3 15.9 - - + -
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Residues in contact with SER 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G GLY 3.5 6.7 - - - -
129G THR* 4.8 0.7 - - - +
130G ALA 4.6 0.7 - - - -
181G LEU* 1.3 77.3 - - - +
183G LYS* 1.3 63.1 + - - +
184G ALA* 3.7 11.4 + - - +
185G ASP* 3.1 32.4 + - - -
186G TYR* 3.2 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