Contacts of the helix formed by residues 114 - 120 (chain D) in PDB entry 2Y05
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D PHE* 5.7 4.3 - - + -
109D TRP* 3.7 5.6 - - - -
113D ILE* 1.3 91.5 - - + +
115D LEU* 1.3 64.3 + - - +
116D SER* 3.2 20.2 + - - +
117D LEU* 3.3 23.5 + - + +
298D TYR* 3.5 31.0 - - + +
300D GLU* 3.5 17.9 - - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.9 27.4 - - + -
43D PHE* 4.3 14.6 - - + -
68D VAL* 3.5 17.9 - - + +
84D ILE* 4.0 25.1 - - + -
105D LEU* 4.3 15.9 - - + +
109D TRP* 4.0 23.9 - - + +
110D PRO 5.6 0.4 - - - +
111D ASP* 6.5 0.9 - - - -
113D ILE 3.6 3.0 + - - +
114D PRO* 1.3 72.4 - - - +
116D SER* 1.3 56.0 + - - +
117D LEU 3.1 4.3 + - - -
118D ALA* 3.2 23.9 + - - +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 3.8 34.3 - - - -
68D VAL* 4.4 9.6 - - - -
114D PRO* 3.5 7.4 - - - +
115D LEU* 1.3 72.3 - - - +
117D LEU* 1.3 64.3 + - - +
118D ALA 2.9 2.2 - - - -
119D LEU* 2.9 17.9 + - - +
120D GLY* 3.4 6.4 + - - -
300D GLU* 2.4 37.6 + - - +
302D ILE* 5.1 0.5 - - - +
324D LYS* 5.4 0.2 - - - +
326D ILE* 4.0 17.5 - - - +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TRP* 3.9 12.1 - - + -
113D ILE* 4.2 14.4 - - + -
114D PRO* 3.3 21.7 + - + +
115D LEU 3.1 1.4 - - - -
116D SER* 1.3 77.7 - - - +
118D ALA* 1.3 57.6 + - - +
119D LEU 3.1 0.2 - - - -
120D GLY* 2.9 18.6 + - - +
121D THR* 4.6 9.0 - - - +
122D VAL* 3.1 33.2 + - + +
291D VAL* 4.1 18.4 - - + -
298D TYR* 3.9 45.1 - - + -
300D GLU* 3.6 26.9 - - + +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLN* 4.5 2.4 - - - +
68D VAL* 4.3 1.8 - - + -
86D LEU* 4.1 18.5 - - + +
105D LEU* 3.9 15.3 - - + -
109D TRP* 3.4 15.0 - - + -
115D LEU 3.2 17.1 + - - +
116D SER 2.9 0.2 - - - -
117D LEU* 1.3 78.7 - - - +
119D LEU* 1.3 56.9 + - - +
120D GLY 3.4 0.2 - - - -
122D VAL 3.5 11.6 - - - +
123D GLY* 3.5 15.9 - - - -
124D MET 4.4 1.0 + - - -
1331D EDO 3.9 19.8 + - - -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 3.4 37.5 - - + +
44D LEU 3.9 2.0 - - - -
45D THR* 3.8 27.7 + - + +
47D ASP* 5.1 0.2 - - - +
66D GLN* 3.7 23.1 - - + +
67D GLN* 3.8 15.3 - - - +
68D VAL* 3.8 9.6 - - + +
86D LEU* 3.6 27.1 - - + -
116D SER* 2.9 11.1 + - - +
118D ALA* 1.3 75.7 - - - +
120D GLY* 1.3 54.5 + - - +
124D MET* 4.7 1.0 - - - +
125D PRO* 3.1 20.2 - - - +
324D LYS* 3.3 15.5 - - - -
326D ILE* 3.9 15.7 - - + -
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Residues in contact with GLY 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER 3.4 4.5 + - - -
117D LEU* 2.9 5.8 + - - -
118D ALA 3.4 0.2 - - - -
119D LEU* 1.3 79.3 - - - +
121D THR* 1.3 59.4 + - - -
122D VAL 3.2 2.2 - - - -
123D GLY 2.9 21.0 + - - -
125D PRO* 3.5 10.9 - - - +
126D GLY 3.0 18.0 + - - -
153D ALA* 5.6 1.3 - - - -
324D LYS* 4.1 17.7 - - - -
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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