Contacts of the helix formed by residues 37 - 48 (chain B) in PDB entry 2Y96
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 GLY 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ARG* 3.7 13.0 - - - +
35B THR 3.7 1.2 + - - -
36B PRO* 1.3 76.9 - - - +
38B ALA* 1.3 66.8 + - - -
39B PHE 3.4 1.8 - - - -
40B GLU* 3.3 8.6 + - - +
41B LEU* 3.0 20.8 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 5.5 13.2 - - + +
190A LEU* 4.6 11.8 - - + +
194A ARG* 4.5 7.2 - - - +
37B GLY* 1.3 68.9 - - - -
39B PHE* 1.3 67.2 + - - +
41B LEU* 3.1 13.0 + - - +
42B GLU* 2.9 33.2 + - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLY 3.4 0.4 - - - -
38B ALA* 1.3 78.7 - - - +
40B GLU* 1.3 73.7 + - + +
42B GLU* 3.3 8.7 + - + +
43B ARG* 3.1 53.7 + - + +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 4.2 15.3 - - + -
37B GLY* 3.3 11.0 + - - +
38B ALA 3.2 0.2 - - - -
39B PHE* 1.3 85.9 - - + +
41B LEU* 1.3 66.1 + - - +
43B ARG* 2.7 52.9 + - - +
44B LEU* 3.3 28.1 + - + +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 4.0 16.4 - - + -
171A VAL* 4.7 1.8 - - + -
174A ILE* 3.8 22.4 - - + +
190A LEU* 4.1 23.6 - - + -
194A ARG* 3.4 40.6 - - + -
36B PRO* 3.5 30.1 - - + +
37B GLY 3.0 16.0 + - - +
38B ALA* 3.5 8.1 - - - +
40B GLU* 1.3 75.0 - - - +
42B GLU* 1.3 63.7 + - - +
44B LEU* 3.0 26.1 + - + +
45B PHE* 3.2 14.5 + - + -
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.1 21.7 - - + +
185A PRO 4.9 3.6 - - - +
187A ARG* 3.6 28.3 + - - +
190A LEU* 3.7 22.4 - - + +
38B ALA* 2.9 19.6 + - - +
39B PHE* 3.7 7.2 - - + +
40B GLU 3.3 0.2 - - - -
41B LEU* 1.3 75.6 - - - +
43B ARG* 1.3 64.2 + - - +
45B PHE* 3.1 13.8 + - + +
46B TRP* 3.2 28.1 + - + -
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.1 40.7 + - + +
40B GLU* 2.7 50.7 + - - +
41B LEU 3.3 0.6 - - - -
42B GLU* 1.3 74.4 - - - +
44B LEU* 1.3 61.6 + - + +
46B TRP* 4.6 5.2 - - - +
47B LYS* 2.7 50.6 + - + +
48B GLY* 3.5 0.6 + - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.0 32.8 - - + -
174A ILE* 4.1 24.5 - - + +
175A GLN* 4.6 22.4 - - - +
178A ALA* 4.5 5.4 - - - +
36B PRO* 5.0 2.5 - - + -
40B GLU* 3.3 18.6 + - - +
41B LEU* 3.0 25.0 + - + +
43B ARG* 1.3 87.3 - - + +
45B PHE* 1.3 59.6 + - - +
48B GLY* 3.1 28.2 + - - +
49B SER* 4.6 0.9 + - - -
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 4.1 8.3 - - + -
174A ILE* 3.5 45.1 - - + -
178A ALA* 4.6 12.4 - - + +
182A CYS* 6.0 0.9 - - - -
183A VAL* 3.3 44.8 + - + +
184A LEU* 3.9 19.5 - - + -
185A PRO* 3.5 28.3 - - + -
190A LEU* 3.6 27.4 - - + -
41B LEU 3.2 22.8 + - - -
42B GLU* 3.1 12.7 + - + +
44B LEU* 1.3 78.1 - - - +
46B TRP* 1.3 60.8 + - + +
49B SER* 6.1 0.2 - - - -
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Residues in contact with TRP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 4.0 36.1 - - + +
42B GLU* 3.2 30.4 + - + +
43B ARG* 3.8 3.8 - - - +
44B LEU 3.2 0.4 - - - -
45B PHE* 1.3 81.7 - - - +
47B LYS* 1.3 77.9 + - + +
48B GLY 3.7 0.2 - - - -
49B SER 4.9 5.8 - - - +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 2.7 32.0 + - + +
46B TRP* 1.3 89.0 - - + +
48B GLY* 1.3 61.8 + - - +
49B SER 3.2 6.4 + - - +
50B PRO 4.3 6.2 - - - +
51B GLN* 5.4 0.5 - - - -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLN* 3.2 23.9 + - - +
43B ARG* 3.5 2.4 + - - -
44B LEU* 3.1 30.4 + - - -
46B TRP 3.7 0.2 - - - -
47B LYS* 1.3 78.0 - - - +
49B SER* 1.3 60.7 + - - +
50B PRO 4.0 2.0 - - - -
51B GLN* 3.4 21.5 + - - +
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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