Contacts of the helix formed by residues 45 - 59 (chain D) in PDB entry 2IYL
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU 4.4 1.6 + - - -
40D LEU* 4.0 10.1 + - - +
43D ASP* 3.1 7.4 - - - +
44D VAL* 1.3 80.8 - - - +
46D LEU* 1.3 64.7 + - - -
47D SER 3.4 2.0 + - - -
48D ALA 3.6 1.1 + - - -
49D THR* 2.8 32.6 + - - -
268D PRO* 5.5 1.8 - - - -
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Residues in contact with LEU 46 (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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36D GLU* 4.8 11.2 - - - +
40D LEU* 3.9 23.3 - - + +
45D GLY* 1.3 71.0 - - - -
47D SER* 1.3 59.5 + - - +
49D THR* 3.3 3.2 + - + -
50D GLU* 2.9 66.6 + - + +
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Residues in contact with SER 47 (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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45D GLY 3.4 0.4 - - - -
46D LEU* 1.3 79.7 - - - +
48D ALA* 1.3 61.8 + - - +
50D GLU* 3.9 9.8 - - - +
51D GLU* 3.2 24.6 + - - +
271D ARG* 4.0 14.2 + - - -
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Residues in contact with ALA 48 (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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44D VAL* 3.6 21.1 + - + +
45D GLY 3.6 2.4 + - - -
46D LEU 3.5 0.2 - - - -
47D SER* 1.3 74.9 - - - +
49D THR* 1.3 60.1 + - - +
51D GLU* 3.2 4.2 + - - +
52D ILE* 2.9 34.5 + - - +
75D MET* 3.7 9.2 - - + -
267D ILE* 3.8 10.3 - - + -
268D PRO* 5.0 3.6 - - + -
271D ARG* 3.5 35.5 - - - +
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Residues in contact with THR 49 (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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36D GLU* 3.8 42.0 - - + +
39D LEU* 3.5 34.2 - - + +
40D LEU* 3.8 12.7 - - + +
44D VAL* 3.6 7.6 - - - +
45D GLY 2.8 23.6 + - - -
46D LEU* 3.7 4.0 - - + -
48D ALA* 1.3 76.9 - - - +
50D GLU* 1.3 64.1 + - + +
52D ILE* 3.2 4.2 + - - +
53D LEU* 3.0 30.6 + - + +
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Residues in contact with GLU 50 (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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36D GLU* 5.7 1.3 - - - +
46D LEU* 2.9 56.4 + - + +
47D SER* 3.9 7.4 - - - +
49D THR* 1.3 71.1 - - + +
51D GLU* 1.3 53.7 + - - +
53D LEU* 3.2 14.8 + - + +
54D GLN* 2.8 45.9 + - + +
57D ARG* 5.2 0.7 + - - +
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Residues in contact with GLU 51 (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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47D SER* 3.2 8.9 + - - +
48D ALA 3.2 10.3 + - - +
50D GLU* 1.3 78.0 - - - +
52D ILE* 1.3 63.3 + - + +
54D GLN* 3.6 16.8 + - - +
55D GLU* 2.9 39.8 + - - +
75D MET* 5.4 0.4 - - + -
271D ARG* 3.3 38.6 + - - +
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Residues in contact with ILE 52 (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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35D LEU* 3.8 27.4 - - + -
39D LEU* 4.1 11.7 - - + -
44D VAL* 4.8 2.5 - - + -
48D ALA* 2.9 39.6 + - + +
49D THR* 3.2 7.8 + - - +
51D GLU* 1.3 72.2 - - - +
53D LEU* 1.3 59.6 + - - +
55D GLU* 3.4 5.5 - - - +
56D VAL* 2.8 42.3 + - + +
68D VAL* 4.8 8.1 - - + -
71D LYS* 4.7 12.6 - - + -
72D LEU* 3.7 25.6 - - + -
75D MET* 3.4 31.6 - - + -
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Residues in contact with LEU 53 (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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32D LEU* 3.5 47.2 - - + +
35D LEU* 4.1 11.7 - - + -
36D GLU* 3.9 37.5 - - + +
49D THR* 3.0 28.7 + - + +
50D GLU* 3.5 15.5 - - + +
52D ILE* 1.3 77.9 - - + +
54D GLN* 1.3 64.4 + - - +
56D VAL* 3.8 1.6 - - - +
57D ARG* 3.2 43.7 + - - +
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Residues in contact with GLN 54 (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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50D GLU* 2.8 28.8 + - + +
51D GLU* 3.6 22.1 + - - +
53D LEU* 1.3 73.9 - - - +
55D GLU* 1.3 65.0 + - - +
56D VAL 3.1 1.2 + - - -
57D ARG* 3.3 32.7 + - - +
58D ALA* 3.3 14.2 + - - +
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Residues in contact with GLU 55 (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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51D GLU* 2.9 33.7 + - - +
52D ILE* 3.4 7.4 - - - +
54D GLN* 1.3 72.6 - - - +
56D VAL* 1.3 60.3 + - - +
58D ALA* 3.6 6.0 - - - +
59D SER* 3.1 32.1 + - - -
71D LYS* 3.1 45.7 + - + +
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Residues in contact with VAL 56 (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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28D LEU* 5.4 2.2 - - + +
31D VAL* 6.5 0.2 - - + -
32D LEU* 3.9 21.5 - - + -
35D LEU* 4.8 0.4 - - + -
52D ILE* 2.8 40.0 + - + +
53D LEU 3.8 4.3 - - - +
55D GLU* 1.3 71.3 - - - +
57D ARG* 1.3 66.6 + - - +
59D SER* 2.9 21.6 - - - +
64D LEU* 4.5 23.9 - - + +
67D ALA* 5.0 8.7 - - + +
68D VAL* 3.8 26.5 - - + +
71D LYS* 4.3 17.5 - - + +
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Residues in contact with ARG 57 (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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28D LEU* 4.7 20.0 - - + +
32D LEU* 3.4 29.1 - - + +
50D GLU 5.2 0.2 + - - -
53D LEU* 3.2 37.3 + - - +
54D GLN* 3.5 34.7 + - - +
56D VAL* 1.3 76.5 - - - +
58D ALA* 1.3 70.6 + - - +
59D SER 3.1 6.2 + - - +
60D GLY* 3.9 3.5 + - - -
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Residues in contact with ALA 58 (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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54D GLN 3.3 9.8 + - - +
55D GLU* 3.6 12.3 - - - +
57D ARG* 1.3 78.9 - - - +
59D SER* 1.3 58.5 + - - +
60D GLY* 3.0 10.6 + - - -
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Residues in contact with SER 59 (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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55D GLU* 3.1 18.5 + - - -
56D VAL* 2.9 18.8 - - - +
57D ARG 3.1 2.0 + - - +
58D ALA* 1.3 73.6 - - - +
60D GLY* 1.3 58.5 + - - +
61D ARG* 2.8 21.0 + - - +
67D ALA* 5.5 6.1 - - - +
71D LYS* 3.5 26.2 + - - -
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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