Contacts of the helix formed by residues 35 - 47 (chain A) in PDB entry 6YBO
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 ASP 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG* 4.5 4.7 - - - +
33A ALA 4.0 1.4 + - - -
34A LEU* 1.3 73.9 - - - +
36A PRO* 1.3 77.1 - - - +
37A VAL* 3.0 15.4 + - - +
38A GLU* 2.9 26.1 + - + +
39A SER* 3.2 10.2 + - - -
74A ARG* 2.6 40.8 + - - -
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Residues in contact with PRO 36 (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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15A LEU* 4.0 29.7 - - + +
34A LEU 3.6 7.2 - - - +
35A ASP* 1.3 89.8 - - - +
37A VAL* 1.3 60.0 + - + +
39A SER* 3.3 5.6 + - - +
40A VAL* 3.0 28.7 + - - +
57A ASP 4.0 20.9 - - - +
58A LEU* 4.5 13.5 - - + +
74A ARG* 5.2 2.5 - - - +
75A PHE* 4.3 13.2 - - + -
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Residues in contact with VAL 37 (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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35A ASP* 3.0 10.7 + - - +
36A PRO* 1.3 76.6 - - + +
38A GLU* 1.3 63.2 + - - +
40A VAL* 3.4 3.8 + - - +
41A ARG* 3.1 58.9 + - - +
74A ARG* 3.6 59.9 - - + +
75A PHE* 4.4 5.2 - - - +
78A ALA* 3.9 17.9 - - + -
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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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32A ARG* 3.2 31.1 + - - -
34A LEU* 3.9 15.7 - - + +
35A ASP* 2.9 22.0 + - + +
37A VAL* 1.3 79.9 - - - +
39A SER* 1.3 58.2 + - - +
41A ARG* 3.2 12.9 + - + +
42A ARG* 2.9 53.7 + - + +
300A TRP* 5.3 2.8 + - + -
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Residues in contact with SER 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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15A LEU* 4.1 20.2 + - - +
18A VAL* 4.0 16.9 - - - +
34A LEU* 3.4 32.9 - - - +
35A ASP 3.2 4.8 + - - -
36A PRO* 3.3 9.3 + - - +
38A GLU* 1.3 78.1 - - - +
40A VAL* 1.3 58.2 + - - +
42A ARG* 3.8 0.3 - - - +
43A LEU* 2.9 38.7 + - - +
300A TRP* 4.2 10.1 - - - -
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Residues in contact with VAL 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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15A LEU* 4.7 2.2 - - + -
36A PRO 3.0 20.5 + - - +
37A VAL 3.7 5.2 - - - +
38A GLU 3.3 0.2 - - - -
39A SER* 1.3 73.8 - - - +
41A ARG* 1.3 63.4 + - - +
43A LEU* 3.9 1.0 - - - +
44A ALA* 3.0 23.9 + - - +
51A VAL* 4.1 18.4 - - + -
75A PHE* 3.6 29.4 - - + -
78A ALA* 3.9 22.0 - - + +
79A LEU* 4.3 3.6 - - + -
82A THR* 3.6 24.0 - - + +
84A MET* 4.0 20.2 - - + +
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Residues in contact with ARG 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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37A VAL* 3.1 39.9 + - + +
38A GLU* 3.2 11.1 + - + +
40A VAL* 1.3 76.8 - - - +
42A ARG* 1.3 65.2 + - + +
44A ALA* 3.3 3.6 + - - +
45A GLU* 3.1 33.4 + - - +
78A ALA* 5.1 6.5 - - + +
81A ASP* 4.9 13.9 + - + +
82A THR* 4.2 20.6 - - + -
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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 41.9 + - + +
39A SER 4.0 0.2 - - - +
41A ARG* 1.3 77.9 - - + +
43A LEU* 1.3 62.3 + - - +
45A GLU* 3.2 25.1 + - - +
46A LEU* 3.2 28.4 + - - +
297A ASP* 5.4 4.8 + - - -
300A TRP* 3.4 68.3 - - + +
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Residues in contact with LEU 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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13A PHE* 3.7 45.3 - - + +
14A GLY 5.4 0.9 - - - +
15A LEU* 5.8 1.3 - - + -
18A VAL* 4.3 19.7 - - + -
39A SER* 2.9 24.2 + - - +
42A ARG* 1.3 73.2 - - - +
44A ALA* 1.3 65.8 + - - +
46A LEU* 3.1 23.3 + - + +
47A GLY 3.3 0.2 + - - -
48A ALA* 3.1 24.4 + - + +
51A VAL* 3.6 26.0 - - + -
84A MET* 3.9 13.0 - - + -
300A TRP* 4.1 19.5 - - + -
303A ALA* 4.6 0.9 - - + -
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Residues in contact with ALA 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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7A PRO* 6.1 0.5 - - - +
40A VAL 3.0 18.9 + - - +
41A ARG 3.6 4.7 - - - +
43A LEU* 1.3 77.7 - - - +
45A GLU* 1.3 61.7 + - + +
47A GLY* 3.1 14.4 + - - -
48A ALA 4.5 3.0 - - - +
82A THR* 3.8 31.0 - - + +
84A MET* 3.8 18.5 - - + -
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Residues in contact with GLU 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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4A GLN* 5.5 1.7 + - - -
41A ARG* 3.1 19.1 + - + +
42A ARG* 3.6 33.8 + - - +
43A LEU 3.2 0.2 - - - -
44A ALA* 1.3 78.0 - - + +
46A LEU* 1.3 62.1 + - + +
47A GLY 3.5 0.7 + - - -
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Residues in contact with LEU 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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4A GLN* 3.8 9.1 + - - -
5A PRO* 3.5 21.0 - - - +
42A ARG* 3.2 15.2 + - - +
43A LEU* 3.1 16.1 + - + +
45A GLU* 1.3 78.6 - - + +
47A GLY* 1.3 58.4 + - - +
48A ALA 3.6 0.2 - - - -
300A TRP* 3.9 46.4 - - + +
303A ALA* 4.2 11.9 - - + -
304A ALA* 4.3 18.8 - - + +
307A MET* 3.6 14.0 - - + +
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Residues in contact with GLY 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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4A GLN* 4.8 1.1 - - - -
5A PRO* 3.9 18.3 - - - +
6A THR* 3.4 28.6 + - - +
7A PRO* 4.5 5.6 - - - -
11A PHE* 5.0 1.7 - - - +
44A ALA 3.1 12.6 + - - -
45A GLU 3.3 1.2 + - - -
46A LEU* 1.3 80.0 - - - +
48A ALA* 1.3 66.0 + - - +
307A MET* 4.4 5.1 - - - +
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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