Contacts of the helix formed by residues 37 - 46 (chain A) in PDB entry 2PID
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 1.3 56.6 + - - -
39A LEU 3.4 2.0 - - - -
40A ALA* 3.0 19.2 + - - +
41A ALA* 2.5 40.4 + - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY* 1.3 72.2 - - - +
39A LEU* 1.3 68.2 + - + +
41A ALA* 3.0 4.2 + - + +
42A GLN* 3.0 48.8 + - + +
48A PHE* 5.3 0.7 - - + -
65A PHE* 4.5 11.2 - - + -
100A HIS* 3.9 18.2 - - + +
101A LEU* 3.4 31.2 - - + -
104A ALA* 3.6 28.7 - - + -
106A HIS* 4.2 12.1 - - + +
163A ARG* 6.1 0.7 - - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY 3.4 0.4 - - - -
38A LEU* 1.3 79.8 - - + +
40A ALA* 1.3 58.5 + - - +
42A GLN* 3.4 1.6 + - - +
43A LYS* 2.9 33.1 + - - +
48A PHE* 3.9 20.2 - - + -
51A PHE* 3.5 35.9 - - + -
61A LEU* 3.9 15.0 - - + -
62A PRO* 3.7 40.8 - - + -
65A PHE* 3.9 27.6 - - + +
101A LEU* 5.5 2.2 - - + -
269A ILE* 4.4 9.6 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLY* 3.0 26.1 + - - +
39A LEU* 1.3 79.7 - - - +
41A ALA* 1.3 56.4 - - - +
43A LYS* 3.5 7.0 - - - +
44A ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY 2.5 21.6 + - - +
38A LEU* 3.5 6.5 - - + +
40A ALA* 1.3 73.8 - - - +
42A GLN* 1.3 65.9 + - - +
44A ALA* 3.0 9.4 + - - +
45A ARG* 2.8 34.3 + - + +
326A LEU* 5.2 10.0 - - + +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.0 30.8 + - + +
41A ALA* 1.3 79.1 - - - +
43A LYS* 1.3 67.0 + - - +
45A ARG* 3.3 17.8 + - - +
46A GLY 2.9 18.4 + - - -
47A LEU* 3.1 30.0 + - - +
48A PHE* 3.3 45.9 + - + +
100A HIS* 3.0 41.7 - - + -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 2.9 17.7 + - - +
40A ALA* 3.5 7.4 - - - +
42A GLN* 1.3 76.2 - - - +
44A ALA* 1.3 63.1 + - - +
46A GLY* 3.1 13.2 + - - -
48A PHE* 3.6 12.7 + - - +
49A LYS* 3.1 28.6 + - - +
50A ASP* 4.8 3.3 - - - +
51A PHE* 3.4 33.0 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA 2.9 15.0 + - - +
41A ALA* 3.2 12.6 - - - +
43A LYS* 1.3 76.1 - - - +
45A ARG* 1.3 64.2 + - - +
46A GLY* 3.3 0.7 + - - -
319A LYS* 3.8 13.5 + - - -
326A LEU* 4.3 17.3 - - + -
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 2.8 20.5 + - - +
42A GLN* 3.6 31.9 + - - +
44A ALA* 1.3 73.1 - - - +
46A GLY* 1.3 58.8 + - - +
47A LEU* 3.3 6.3 - - + +
100A HIS* 4.2 11.9 + - - -
316A ARG* 5.4 1.4 - - - +
318A LEU 4.0 2.2 + - - -
319A LYS* 2.9 66.1 + - + +
320A LEU* 3.4 14.9 - - - +
322A THR 3.4 15.2 + - - -
323A PHE* 3.5 9.4 + - - +
324A LEU 2.4 37.6 + - - -
325A PRO* 3.8 7.7 - - - +
326A LEU* 3.9 25.8 - - + +
329A ILE* 4.1 2.6 - - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN 2.9 4.0 + - - -
43A LYS 3.1 10.1 + - - -
44A ALA 3.1 4.3 - - - -
45A ARG* 1.3 79.9 - - - +
47A LEU* 1.3 63.2 + - - +
48A PHE 3.4 8.7 - - - -
49A LYS* 4.3 2.5 + - - -
272A PRO* 3.2 22.3 - - - +
320A LEU* 3.6 7.5 - - - +
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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