Contacts of the helix formed by residues 162 - 175 (chain K) in PDB entry 6Y5D
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 ALA 162 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161K GLY* 1.3 79.0 - - - +
163K SER* 1.3 59.6 + - - +
164K LYS 3.4 0.2 - - - -
165K LEU* 3.2 6.7 + - - +
166K ARG* 2.9 37.3 + - + +
457K ARG 4.8 1.6 - - - +
458K LYS 4.1 16.8 - - - +
460K LEU* 3.9 11.8 - - + +
461K GLY* 3.7 21.4 - - - +
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Residues in contact with SER 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K GLY* 3.5 2.2 - - - +
162K ALA* 1.3 77.5 - - - +
164K LYS* 1.3 62.6 + - - +
166K ARG* 3.2 9.0 + - - +
167K ALA* 3.2 21.0 + - - +
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Residues in contact with LYS 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K GLY* 4.4 6.8 + - - +
162K ALA 3.4 0.4 - - - -
163K SER* 1.3 78.5 - - - +
165K LEU* 1.3 65.2 + - + +
167K ALA* 3.4 8.9 + - + +
168K VAL* 3.2 25.4 + - + +
514K ASN 4.6 1.8 + - - -
515K GLU* 2.8 47.5 + - + +
516K PHE 4.2 8.2 + - - -
517K PRO* 4.4 4.4 - - - +
519K PHE* 5.4 4.3 - - + -
520K ASP* 2.9 34.9 + - - +
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Residues in contact with LEU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K GLY 3.3 22.2 - - - +
162K ALA 3.5 5.6 - - - +
163K SER 3.2 0.2 - - - -
164K LYS* 1.3 79.2 - - + +
166K ARG* 1.3 58.2 + - - +
168K VAL* 3.2 7.3 + - - +
169K LEU* 2.9 31.4 + - - +
412K LEU* 3.8 18.7 - - + +
460K LEU* 3.5 26.7 - - + +
461K GLY* 3.7 22.2 - - - +
464K PHE* 4.0 14.1 - - + -
516K PHE* 4.8 7.2 - - + -
519K PHE* 3.6 33.4 - - + -
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Residues in contact with ARG 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162K ALA* 2.9 23.7 + - + +
163K SER* 3.2 10.7 + - - +
165K LEU* 1.3 75.7 - - - +
167K ALA* 1.3 63.0 + - - +
169K LEU* 3.3 11.5 + - - +
170K GLU* 3.0 26.9 + - - +
403K LYS* 5.2 3.6 - - - +
405K CYS* 4.4 0.8 - - - +
408K ASP* 2.7 34.9 + - - -
457K ARG* 2.9 61.9 + - - +
460K LEU* 3.7 17.9 - - + +
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Residues in contact with ALA 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K SER 3.2 9.9 + - - +
164K LYS* 3.6 10.8 - - - +
165K LEU 3.3 0.2 - - - -
166K ARG* 1.3 78.3 - - - +
168K VAL* 1.3 63.4 + - + +
170K GLU* 3.4 7.5 + - - +
171K LYS* 3.0 25.3 + - - +
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Residues in contact with VAL 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K LYS* 3.2 16.5 + - + +
165K LEU* 3.2 10.9 + - - +
167K ALA* 1.3 79.5 - - + +
169K LEU* 1.3 57.4 + - - +
171K LYS* 3.2 13.1 + - - +
172K LEU* 2.9 34.2 + - + +
412K LEU* 4.0 10.1 - - + -
415K TYR* 3.3 36.6 - - + +
519K PHE* 3.8 35.0 - - + +
520K ASP* 4.5 8.7 - - - +
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Residues in contact with LEU 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K LEU 2.9 19.4 + - - +
166K ARG* 3.7 10.8 - - - +
168K VAL* 1.3 76.2 - - - +
170K GLU* 1.3 62.3 + - - +
172K LEU* 3.3 9.5 + - + +
173K LYS* 3.1 23.9 + - - +
408K ASP* 3.5 46.7 - - + +
411K LYS* 3.6 39.7 - - + +
412K LEU* 4.0 14.1 - - + +
460K LEU* 3.8 17.7 - - + -
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Residues in contact with GLU 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K ARG 3.0 17.2 + - - +
167K ALA* 3.7 6.4 - - - +
169K LEU* 1.3 76.3 - - - +
171K LYS* 1.3 63.8 + - - +
173K LYS* 3.4 4.9 + - - +
174K LEU* 3.0 50.7 + - + +
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Residues in contact with LYS 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K ALA 3.0 17.5 + - - +
168K VAL* 3.4 16.8 - - - +
170K GLU* 1.3 77.4 - - - +
172K LEU* 1.3 66.0 + - - +
174K LEU* 3.4 8.5 + - - +
175K SER* 3.2 23.4 + - - -
415K TYR* 3.8 14.9 + - - -
519K PHE 2.9 26.7 + - - -
520K ASP* 4.1 16.0 + - - +
522K PHE 5.6 5.0 + - - -
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Residues in contact with LEU 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K VAL* 2.9 31.3 + - + +
169K LEU* 3.3 16.5 + - + +
171K LYS* 1.3 80.1 - - + +
173K LYS* 1.3 60.6 + - - +
175K SER* 2.7 26.4 + - - +
176K ARG* 3.7 11.7 + - - -
220K ILE* 3.8 41.7 - - + +
221K SER* 4.3 5.8 - - - -
411K LYS* 4.7 3.6 - - + +
412K LEU* 5.6 0.2 - - + -
415K TYR* 3.5 51.6 - - + -
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Residues in contact with LYS 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K LEU 3.1 13.4 + - - +
170K GLU* 3.9 4.9 - - - +
172K LEU* 1.3 79.4 - - - +
174K LEU* 1.3 61.8 + - + +
176K ARG* 2.9 31.3 + - - +
177K ASP* 3.9 10.2 + - - +
220K ILE* 5.5 2.9 - - - +
411K LYS* 6.3 3.1 - - + -
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Residues in contact with LEU 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K GLU* 3.0 51.6 + - + +
171K LYS* 3.8 7.6 - - - +
173K LYS* 1.3 79.1 - - + +
175K SER* 1.3 58.4 + - - +
176K ARG 2.9 5.5 + - - -
177K ASP* 3.0 38.8 + - - +
178K ASP* 4.5 3.6 + - - +
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Residues in contact with SER 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K LYS 3.2 12.5 + - - -
172K LEU* 2.7 25.2 + - - +
174K LEU* 1.3 75.5 - - - +
176K ARG* 1.3 66.5 + - - +
177K ASP 3.4 0.2 - - - -
178K ASP* 4.2 18.5 + - - +
179K ILE* 4.4 1.7 - - - +
220K ILE 4.9 0.9 + - - -
221K SER* 6.1 0.2 - - - -
223K PRO* 4.0 23.9 - - - +
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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