Contacts of the helix formed by residues 37 - 52 (chain A) in PDB entry 2FY2
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 1.3 79.8 - - - +
38A GLU* 1.3 60.1 + - - +
39A GLU* 3.8 6.8 + - - +
40A GLN* 2.9 35.9 + - - +
41A PHE* 2.8 26.9 + - - +
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Residues in contact with GLU 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 SER* 1.3 70.6 - - - +
39A GLU* 1.3 61.3 + - - +
41A PHE* 3.3 7.5 + - - +
42A ARG* 2.9 56.7 + - - +
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Residues in contact with GLU 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 SER* 3.3 7.3 - - - +
38A GLU* 1.3 80.3 - - - +
40A GLN* 1.3 62.8 + - - +
42A ARG* 3.3 13.7 + - - +
43A LYS* 3.1 55.9 + - - +
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Residues in contact with GLN 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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36A VAL* 3.8 19.0 - - + +
37A SER* 2.9 26.7 + - - +
39A GLU* 1.3 76.4 - - - +
41A PHE* 1.3 58.8 + - - +
43A LYS* 3.1 14.4 + - + +
44A SER* 2.9 27.3 + - - +
526A ASP* 5.0 3.1 - - - +
527A GLU* 3.8 19.0 - - - +
528A THR* 3.0 39.0 + - - +
531A MET* 5.4 1.4 - - - +
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Residues in contact with PHE 41 (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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29A LEU* 3.6 30.5 - - + -
32A MET* 4.8 2.0 - - + -
33A ARG* 3.3 74.7 - - + +
36A VAL* 3.9 12.3 - - + +
37A SER 2.8 18.5 + - - +
38A GLU* 3.3 8.3 + - - +
40A GLN* 1.3 77.1 - - - +
42A ARG* 1.3 60.5 + - + +
44A SER* 3.0 7.9 + - - +
45A GLN* 2.8 74.7 + - + +
528A THR* 6.3 0.4 - - + -
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Residues in contact with ARG 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 GLU* 2.9 48.1 + - - +
39A GLU* 3.3 12.1 + - - +
41A PHE* 1.3 77.5 - - + +
43A LYS* 1.3 63.6 + - + +
45A GLN* 3.4 20.1 + - - +
46A ALA* 3.3 19.9 + - - +
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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 GLU* 3.1 45.6 + - - +
40A GLN* 3.4 13.4 - - + +
41A PHE 3.1 0.2 - - - -
42A ARG* 1.3 75.1 - - + +
44A SER* 1.3 60.4 + - - +
46A ALA* 3.3 6.9 + - - +
47A ILE* 3.0 40.0 + - + +
526A ASP* 5.9 1.6 - - - +
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Residues in contact with SER 44 (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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28A TYR* 5.7 1.1 - - - -
29A LEU* 4.2 11.7 - - - -
40A GLN 2.9 11.3 + - - -
41A PHE* 3.6 10.8 - - - -
43A LYS* 1.3 74.4 - - - +
45A GLN* 1.3 61.9 + - - +
47A ILE* 3.7 2.2 - - - +
48A VAL* 2.8 38.7 + - - +
526A ASP* 2.5 30.9 + - - -
528A THR* 2.6 30.7 + - - -
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Residues in contact with GLN 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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29A LEU* 4.3 17.4 - - + +
33A ARG* 4.1 8.7 - - - +
41A PHE* 2.8 54.3 + - + +
42A ARG* 3.5 26.2 - - - +
43A LYS 3.2 0.2 - - - -
44A SER* 1.3 77.1 - - - +
46A ALA* 1.3 57.0 - - - +
48A VAL* 3.8 1.4 - - - +
49A GLN* 2.9 30.9 + - - +
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Residues in contact with ALA 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 ARG 3.3 8.3 + - - +
43A LYS* 3.3 10.2 + - - +
44A SER 3.2 0.6 - - - -
45A GLN* 1.3 78.0 - - - +
47A ILE* 1.3 65.1 + - + +
49A GLN* 3.3 11.1 + - + +
50A GLN* 2.9 25.8 + - - +
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Residues in contact with ILE 47 (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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43A LYS* 3.0 28.0 + - + +
44A SER* 3.3 5.1 + - - +
46A ALA* 1.3 78.2 - - + +
48A VAL* 1.3 58.1 + - + +
50A GLN* 3.4 8.6 + - - +
51A PHE* 2.9 26.5 + - - +
522A GLU* 3.5 39.0 - - + +
523A MET* 3.6 37.0 - - - +
526A ASP* 3.8 30.3 - - + +
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Residues in contact with VAL 48 (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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25A LEU* 3.9 37.4 - - + +
28A TYR* 4.0 14.4 - - + -
29A LEU* 3.6 35.2 - - + -
44A SER* 2.8 22.8 + - - +
45A GLN 3.9 2.7 - - - +
47A ILE* 1.3 74.9 - - + +
49A GLN* 1.3 66.6 + - - +
51A PHE* 3.7 6.3 - - - +
52A GLY* 2.9 22.7 + - - -
523A MET* 3.9 17.5 - - + -
526A ASP* 5.6 1.1 - - - +
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Residues in contact with GLN 49 (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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45A GLN 2.9 20.0 + - - +
46A ALA* 3.4 10.8 - - - +
48A VAL* 1.3 78.8 - - - +
50A GLN* 1.3 66.8 + - + +
52A GLY 3.8 1.4 - - - -
53A ALA* 3.2 32.7 + - - +
54A PRO* 5.8 0.2 - - - +
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Residues in contact with GLN 50 (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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46A ALA 2.9 17.8 + - - +
47A ILE* 3.7 7.3 - - - +
49A GLN* 1.3 85.2 - - + +
51A PHE* 1.3 63.5 + - - +
53A ALA* 3.5 12.7 + - - +
56A GLY* 5.0 5.4 - - - -
57A LEU 5.1 0.7 + - - -
522A GLU* 4.5 14.2 - - - +
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Residues in contact with PHE 51 (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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21A LEU* 4.5 8.1 - - + -
25A LEU* 4.2 21.3 - - + -
47A ILE 2.9 17.7 + - - +
48A VAL 3.2 3.6 + - - +
50A GLN* 1.3 79.3 + - - +
52A GLY* 1.3 58.4 + - - +
53A ALA 3.7 0.3 + - - -
56A GLY 4.4 0.2 - - - -
57A LEU* 4.0 24.1 + - + +
58A GLY* 2.8 54.4 + - - -
61A LEU* 3.8 27.8 - - + -
506A LEU* 5.9 0.4 - - + -
509A LEU* 4.6 9.2 - - + -
521A PRO* 4.4 2.2 - - + -
523A MET* 3.6 50.3 - - + -
524A PHE* 4.1 13.7 - + - -
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Residues in contact with GLY 52 (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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21A LEU* 4.5 8.7 - - - -
22A GLN* 2.9 26.4 + - - +
25A LEU* 3.7 23.3 - - - -
48A VAL 2.9 12.3 + - - -
49A GLN 3.8 2.7 - - - -
51A PHE* 1.3 76.9 - - - +
53A ALA* 1.3 63.1 + - - +
54A PRO* 3.9 1.9 - - - +
59A GLU* 4.7 3.4 - - - +
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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