Contacts of the helix formed by residues 52 - 59 (chain K) in PDB entry 2YGD
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 PRO 52 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K PHE* 4.2 11.9 - - + -
51K PRO* 1.4 90.1 - - + +
53K SER* 1.3 68.2 + - - +
54K PHE* 3.1 6.0 + - + -
55K LEU* 3.5 2.6 + - - +
56K ARG* 3.5 18.4 + - - +
152L VAL* 3.7 25.1 - - + -
154L GLY* 5.3 0.7 - - - -
156L GLU* 4.5 8.3 - - - +
159L ILE* 4.8 1.6 - - + -
161L ILE* 3.9 19.0 - - + +
168L ALA* 3.6 17.8 + - + +
169L VAL* 3.9 21.5 - - + +
171L ALA* 4.1 11.9 - - + -
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Residues in contact with SER 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K PRO 6.0 0.3 - - - -
17K PHE* 5.6 9.4 - - - -
51K PRO 3.6 0.2 - - - -
52K PRO* 1.3 74.7 - - - +
54K PHE* 1.3 67.1 + - - +
55K LEU 3.7 0.2 - - - -
56K ARG* 3.9 8.9 - - - -
57K ALA* 3.2 23.9 + - - +
86K PRO* 4.8 5.5 - - - +
139K SER* 4.0 18.3 + - - -
156L GLU* 2.4 31.1 + - - +
161L ILE* 3.5 19.1 - - - +
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Residues in contact with PHE 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ARG* 6.1 0.2 - - - +
16K PRO* 3.3 39.8 - - + +
17K PHE* 4.5 9.2 - - + -
23K LEU* 3.5 43.3 - - + -
24K PHE* 4.5 8.7 - + - -
27K PHE* 4.9 3.4 - + - -
48K TYR 4.0 12.8 - - - -
49K LEU* 3.4 25.2 - - + +
51K PRO* 3.3 52.0 - - + +
52K PRO* 3.1 1.0 + - + -
53K SER* 1.3 87.2 - - - +
55K LEU* 1.3 60.4 + - - +
56K ARG 3.3 1.1 - - - -
57K ALA* 3.4 8.5 - - - +
58K PRO* 3.1 21.7 - - - +
156L GLU* 6.0 0.2 - - - -
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Residues in contact with LEU 55 (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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9K TRP* 6.5 0.2 - - - -
49K LEU* 4.2 9.5 + - + +
51K PRO 3.7 2.0 + - - -
52K PRO 3.5 2.2 + - - +
54K PHE* 1.3 75.3 - - - +
56K ARG* 1.3 84.4 + - - +
57K ALA 3.2 0.7 - - - -
58K PRO* 3.2 23.1 - - + +
59K SER* 3.7 7.7 + - - -
47L PHE* 5.7 7.2 - - + +
68L MET* 3.6 47.6 - - + +
69L ARG 4.4 2.7 - - - +
167L PRO* 3.5 30.1 - - + +
168L ALA* 3.5 22.9 - - + +
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Residues in contact with ARG 56 (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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52K PRO 3.5 6.2 + - - +
53K SER* 3.9 6.7 - - - +
54K PHE 3.3 0.6 - - - -
55K LEU* 1.3 102.6 - - - +
57K ALA* 1.3 55.5 + - - +
59K SER* 3.9 5.3 + - - -
60K TRP* 2.9 25.3 + - - -
62K ASP* 2.7 51.3 + - - -
137K LEU 4.3 2.0 - - - -
138K SER* 3.6 25.7 + - - +
139K SER* 4.1 7.7 + - - +
68L MET 4.8 0.2 + - - -
161L ILE* 2.7 45.3 + - + +
162L THR* 3.7 3.0 - - - +
163L ARG 4.4 1.3 - - - +
165L GLU* 2.8 54.2 + - - +
167L PRO 4.0 1.2 + - - -
169L VAL* 4.0 5.9 - - - +
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Residues in contact with ALA 57 (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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12K ARG* 6.5 0.9 - - + -
16K PRO* 4.8 14.1 - - + +
53K SER 3.2 14.5 + - - +
54K PHE* 3.4 15.9 - - - +
55K LEU 3.2 0.2 - - - -
56K ARG* 1.3 72.8 - - - +
58K PRO* 1.4 65.5 - - + +
60K TRP* 3.3 37.8 + - + +
139K SER* 4.7 5.2 - - - +
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Residues in contact with PRO 58 (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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9K TRP* 3.9 41.3 - - + -
12K ARG* 5.4 20.2 - - + +
49K LEU* 5.7 1.8 - - + -
54K PHE 3.1 25.4 - - - +
55K LEU* 3.2 18.8 - - + +
57K ALA* 1.4 75.7 - - + +
59K SER* 1.3 61.4 + - - +
60K TRP* 3.7 3.3 + - - +
68L MET* 5.9 1.1 - - + -
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Residues in contact with SER 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K LEU* 3.9 8.2 - - - +
56K ARG* 3.6 19.5 + - - -
57K ALA 3.3 0.4 - - - -
58K PRO* 1.3 81.6 - - - +
60K TRP* 1.3 53.2 + - - +
61K PHE* 2.8 8.0 + - - +
62K ASP* 2.4 56.6 + - - -
63K THR* 3.8 7.7 + - - +
163L ARG* 4.8 0.3 + - - -
165L GLU* 4.7 2.4 + - - -
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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