Contacts of the helix formed by residues 162 - 175 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161L GLY* 1.3 80.6 - - - +
163L SER* 1.3 60.1 + - - +
164L LYS 3.4 0.2 - - - -
165L LEU* 3.2 3.8 + - - +
166L ARG* 2.8 35.2 + - + +
457L ARG 4.4 1.8 - - - +
458L LYS* 3.4 28.0 - - - +
460L LEU* 3.9 12.1 - - + +
461L GLY* 3.7 20.1 - - - +
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Residues in contact with SER 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L GLY* 3.5 2.1 - - - +
162L ALA* 1.3 78.5 - - - +
164L LYS* 1.3 62.2 + - - +
166L ARG* 3.2 8.2 + - - +
167L ALA* 3.0 22.2 + - - +
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Residues in contact with LYS 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L GLY 4.4 6.3 + - - +
162L ALA 3.4 0.2 - - - -
163L SER* 1.3 78.2 - - - +
165L LEU* 1.3 66.1 + - + +
167L ALA* 3.3 8.2 + - + +
168L VAL* 3.1 27.7 + - + +
514L ASN 4.5 2.2 + - - -
515L GLU* 2.8 47.8 + - + +
516L PHE* 4.3 8.7 + - + -
517L PRO* 4.3 5.1 - - - +
519L PHE* 5.6 2.0 - - + -
520L ASP* 3.0 31.3 + - - +
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Residues in contact with LEU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L GLY 3.5 20.0 - - - +
162L ALA 3.2 3.1 + - - +
163L SER 3.2 0.6 - - - -
164L LYS* 1.3 77.7 - - + +
166L ARG* 1.3 61.6 + - - +
168L VAL* 3.2 6.8 + - - +
169L LEU* 2.8 32.1 + - - +
412L LEU* 3.8 15.6 - - + +
460L LEU* 3.3 20.9 - - + +
461L GLY* 3.6 22.2 - - - +
464L PHE* 3.7 24.9 - - + -
515L GLU 5.9 0.4 - - - +
516L PHE* 4.2 11.7 - - + -
519L PHE* 3.5 34.1 - - + -
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Residues in contact with ARG 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L ALA* 2.8 26.4 + - + +
163L SER* 3.2 8.0 + - - +
165L LEU* 1.3 73.7 - - - +
167L ALA* 1.3 64.6 + - - +
169L LEU* 3.3 14.5 + - - +
170L GLU* 2.9 26.2 + - - +
403L LYS* 5.6 2.5 - - - +
405L CYS* 3.6 12.9 - - - +
408L ASP* 2.5 37.6 + - - +
457L ARG* 3.2 65.9 + - - +
460L LEU* 3.5 15.2 - - + +
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Residues in contact with ALA 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163L SER 3.0 12.4 + - - +
164L LYS* 3.6 11.7 - - + +
165L LEU 3.3 0.2 - - - -
166L ARG* 1.3 74.7 - - - +
168L VAL* 1.3 62.1 + - - +
170L GLU* 3.5 7.6 + - - +
171L LYS* 3.0 24.0 + - - +
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Residues in contact with VAL 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L LYS* 3.1 18.4 + - + +
165L LEU 3.2 7.8 + - - +
167L ALA* 1.3 77.9 - - + +
169L LEU* 1.3 59.1 + - - +
171L LYS* 3.1 13.0 + - - +
172L LEU* 2.9 30.9 + - + +
412L LEU* 3.9 14.8 - - + -
415L TYR* 3.4 36.1 - - + -
519L PHE* 3.6 32.8 - - + +
520L ASP* 4.4 11.0 - - - +
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Residues in contact with LEU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L LEU 2.8 16.8 + - - +
166L ARG* 3.3 33.0 + - - +
168L VAL* 1.3 70.1 - - - +
170L GLU* 1.3 66.8 + - - +
172L LEU* 3.2 9.2 + - + +
173L LYS* 3.0 24.3 + - - +
408L ASP* 3.5 39.0 - - + +
411L LYS* 3.7 28.9 - - + +
412L LEU* 3.8 14.6 - - + +
460L LEU* 3.5 24.5 - - + -
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Residues in contact with GLU 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG 2.9 17.0 + - - +
167L ALA* 3.8 7.4 - - - +
169L LEU* 1.3 75.3 - - - +
171L LYS* 1.3 58.5 + - - +
173L LYS* 3.3 7.8 + - + +
174L LEU* 2.9 57.1 + - + +
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Residues in contact with LYS 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L ALA 3.0 13.9 + - - +
168L VAL* 3.3 17.3 - - - +
170L GLU* 1.3 76.7 - - - +
172L LEU* 1.3 64.9 + - + +
174L LEU* 3.4 10.0 + - - +
175L SER* 3.1 24.1 + - - -
415L TYR* 3.7 14.1 + - - -
519L PHE 2.8 28.8 + - - -
520L ASP* 4.2 14.6 + - - +
522L PHE 5.6 4.0 + - - -
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Residues in contact with LEU 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L VAL* 2.9 25.7 + - + +
169L LEU* 3.2 20.6 + - + +
171L LYS* 1.3 76.7 - - + +
173L LYS* 1.3 64.4 + - - +
175L SER* 2.7 26.2 + - - +
176L ARG* 3.6 11.2 + - - -
220L ILE* 3.9 39.5 - - + +
221L SER* 4.7 2.7 - - - -
411L LYS* 4.4 7.0 - - + +
412L LEU* 5.3 0.2 - - + -
415L TYR* 3.5 57.0 - - + -
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Residues in contact with LYS 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L LEU 3.0 16.6 + - - +
170L GLU* 3.7 7.0 - - + +
172L LEU* 1.3 76.5 - - - +
174L LEU* 1.3 60.5 + - + +
176L ARG* 2.9 30.2 + - - +
177L ASP* 3.7 10.9 + - - +
220L ILE* 6.2 1.1 - - - -
411L LYS* 6.2 6.7 - - + +
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Residues in contact with LEU 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L GLU* 2.9 52.0 + - + +
171L LYS* 3.8 7.9 - - - +
173L LYS* 1.3 74.2 - - + +
175L SER* 1.3 57.4 + - - +
176L ARG 3.0 4.5 - - - -
177L ASP* 2.9 46.3 + - - +
178L ASP* 4.4 3.5 + - - +
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Residues in contact with SER 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L LYS* 3.1 13.8 + - - -
172L LEU* 2.7 24.3 + - - +
174L LEU* 1.3 75.1 - - - +
176L ARG* 1.3 68.7 + - - +
177L ASP 3.4 0.4 + - - -
178L ASP* 4.2 19.0 + - - +
179L ILE* 4.5 1.9 - - - +
220L ILE 5.0 0.5 + - - -
223L PRO* 4.1 22.7 - - - +
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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