Contacts of the helix formed by residues 50 - 65 (chain B) in PDB entry 1DY7
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ALA* 4.2 0.4 - - - -
48B ALA 4.4 0.2 + - - -
49B LEU* 1.3 76.3 - - - +
51B ASP* 1.3 60.1 + - - +
52B ALA* 3.6 7.0 + - - +
53B GLN* 2.7 42.2 + - - +
54B TYR* 2.8 27.5 + - - +
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Residues in contact with ASP 51 (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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38B ALA* 6.1 0.2 - - - -
39B ALA* 3.2 28.9 + - - +
50B SER* 1.3 73.3 - - - +
52B ALA* 1.3 57.1 + - - +
54B TYR* 3.8 0.9 - - - +
55B ASN* 2.9 42.7 + - - +
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Residues in contact with ALA 52 (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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50B SER* 3.3 6.6 + - - +
51B ASP* 1.3 77.2 - - - +
53B GLN* 1.3 57.5 + - + +
55B ASN* 3.4 4.5 + - - +
56B GLU* 3.0 31.8 + - - +
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Residues in contact with GLN 53 (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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48B ALA 4.4 2.1 - - - +
49B LEU* 3.4 19.9 - - + +
50B SER* 2.7 48.4 + - - +
52B ALA* 1.3 75.9 - - + +
54B TYR* 1.3 58.1 + - - +
56B GLU* 3.3 7.8 + - - +
57B ALA* 3.0 28.9 + - - +
122B LEU* 3.7 33.4 - - + +
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Residues in contact with TYR 54 (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 VAL* 3.5 30.5 - - + -
38B ALA 3.9 7.4 - - - -
39B ALA* 3.8 14.1 - - + -
40B PRO* 3.5 36.2 - - + +
49B LEU* 4.0 11.8 - - + +
50B SER 2.8 20.3 + - - +
51B ASP 3.9 1.1 - - - +
53B GLN* 1.3 70.7 - - - +
55B ASN* 1.3 59.6 + - - +
57B ALA* 3.2 2.2 + - - +
58B ASN* 2.8 28.8 + - - +
73B ARG* 5.2 1.0 + - - -
126B TYR* 3.4 39.7 + + - -
129B LEU* 3.9 26.4 + - + -
130B ASP 4.0 14.9 + - - -
131B PRO* 4.4 8.1 - - - +
132B ALA* 4.6 5.5 + - + +
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Residues in contact with ASN 55 (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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35B GLN 4.2 2.8 - - - +
36B ASP* 3.0 21.8 + - - +
37B VAL* 2.7 54.4 + - - +
38B ALA* 5.1 0.6 - - - +
39B ALA 5.1 0.2 - - - +
51B ASP* 2.9 34.2 + - - +
52B ALA* 4.1 4.3 - - - +
54B TYR* 1.3 77.4 - - - +
56B GLU* 1.3 62.3 + - - +
58B ASN* 3.3 4.9 + - - +
59B LYS* 3.0 25.1 + - - +
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Residues in contact with GLU 56 (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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52B ALA 3.0 18.3 + - - +
53B GLN* 3.6 7.8 - - - +
55B ASN* 1.3 75.7 - - - +
57B ALA* 1.3 63.0 + - - +
59B LYS* 3.5 7.4 + - + +
60B ILE* 3.2 29.9 + - + +
119B GLN* 3.4 30.0 - - - +
122B LEU* 3.6 20.3 - - + +
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Residues in contact with ALA 57 (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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49B LEU* 4.6 1.6 - - + -
53B GLN 3.0 17.2 + - - +
54B TYR* 3.6 3.8 - - - +
56B GLU* 1.3 74.1 - - - +
58B ASN* 1.3 61.7 + - - +
60B ILE* 3.3 2.7 + - - -
61B TYR* 2.8 25.3 + - - +
122B LEU* 4.0 14.3 - - + +
123B MET* 3.4 25.5 - - - +
126B TYR* 3.5 32.1 - - + -
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Residues in contact with ASN 58 (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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32B LEU 4.3 3.6 - - - +
33B ALA 5.0 0.2 - - - +
35B GLN 4.0 10.4 - - - +
37B VAL* 3.7 38.2 - - + +
54B TYR* 2.8 21.9 + - + +
55B ASN* 3.7 5.6 - - - +
57B ALA* 1.3 73.8 - - - +
59B LYS* 1.3 65.9 + - - +
61B TYR* 3.2 1.6 + - - +
62B PHE* 3.1 51.7 + - - -
126B TYR* 2.6 38.2 + - + -
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Residues in contact with LYS 59 (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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33B ALA* 3.6 27.6 - - + +
34B GLN* 6.0 2.7 - - - +
55B ASN 3.0 17.1 + - - +
56B GLU* 3.8 7.2 - - + +
58B ASN* 1.3 78.2 + - - +
60B ILE* 1.3 63.5 + - + +
62B PHE 3.4 0.2 + - - -
63B GLU* 2.9 61.6 + - + +
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Residues in contact with ILE 60 (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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56B GLU* 3.2 24.8 + - + +
57B ALA* 3.6 6.5 - - - +
59B LYS* 1.3 79.2 - - + +
61B TYR* 1.3 64.4 + - - +
63B GLU* 4.6 5.8 - - - +
64B ARG* 2.8 37.2 + - + +
65B CYS* 3.7 4.2 + - - -
115B LEU* 4.1 20.6 - - + -
119B GLN* 4.0 41.1 - - + +
122B LEU* 5.4 1.1 - - + -
123B MET* 3.7 26.0 - - + -
601B HEC 4.5 2.0 - - + -
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Residues in contact with TYR 61 (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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57B ALA 2.8 15.3 + - - +
58B ASN 3.2 4.9 + - - +
60B ILE* 1.3 73.6 - - - +
62B PHE* 1.3 79.5 + + - +
65B CYS* 2.8 52.4 + - + +
66B ALA* 2.9 26.6 + - + -
69B HIS* 3.3 23.1 - - + +
70B GLY 2.7 29.6 + - - -
71B VAL 4.3 1.1 - - - -
73B ARG* 3.3 33.6 - - + +
81B LEU* 4.5 2.9 - - + -
123B MET* 3.8 6.5 - - + +
126B TYR* 3.5 37.7 - + + +
127B LEU* 4.2 9.9 - - + -
601B HEC 5.3 0.7 - - + -
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Residues in contact with PHE 62 (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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32B LEU* 3.7 33.0 - - + -
33B ALA* 3.5 25.6 - - - +
37B VAL* 6.2 0.7 - - + -
58B ASN* 3.1 52.4 + - - +
61B TYR* 1.3 88.8 - + - +
63B GLU* 1.3 61.0 + - - +
66B ALA* 3.9 22.1 + - + +
67B GLY 5.2 1.9 + - - -
71B VAL* 3.6 42.2 - - + -
126B TYR* 3.9 4.9 - - - -
132B ALA 6.1 1.3 - - - -
134B PRO* 5.4 6.5 - - + -
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Residues in contact with GLU 63 (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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33B ALA* 3.3 18.5 - - + +
59B LYS* 2.9 54.9 + - - +
60B ILE* 4.0 3.8 - - - +
62B PHE* 1.3 78.6 - - - +
64B ARG* 1.3 73.6 + - + +
612B GOL 5.7 0.7 + - - -
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Residues in contact with ARG 64 (chain B).
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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60B ILE* 2.8 26.9 + - + +
63B GLU* 1.3 93.4 + - + +
65B CYS* 1.3 62.7 + - - +
66B ALA 3.9 0.2 - - - -
67B GLY* 5.0 2.5 - - - -
109B TRP* 3.6 40.6 - - + -
114B GLU* 3.2 37.4 + - - +
115B LEU* 5.6 4.8 - - + +
601B HEC 3.2 24.5 - - + +
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Residues in contact with CYS 65 (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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60B ILE 3.9 4.3 - - - -
61B TYR* 2.8 48.4 + - + +
64B ARG* 1.3 73.3 - - - +
66B ALA* 1.3 59.4 + - - +
67B GLY 3.1 2.7 - - - -
68B CYS* 3.1 6.3 + - - +
69B HIS* 2.9 30.6 + - + +
123B MET* 4.2 3.8 - - - -
601B HEC 1.8 66.6 - - + -
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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