Contacts of the helix formed by residues 45 - 57 (chain B) in PDB entry 1S89
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 THR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU 3.7 2.4 + - - -
17B VAL* 3.5 22.1 - - + +
44B ALA* 1.3 75.9 - - - +
46B GLY* 1.3 58.9 + - - +
47B THR 3.3 0.8 + - - -
48B THR* 3.5 4.0 + - - -
49B GLY* 2.8 29.3 + - - -
63B MET* 3.8 2.2 - - - +
64B LEU 3.6 6.7 - - - +
66B GLY 4.0 2.0 - - - +
70B GLY* 3.7 32.8 - - - +
71B ASP* 3.9 15.5 - - - +
74B VAL* 4.3 4.7 - - + -
202B PGA 2.7 35.7 + - - -
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Residues in contact with GLY 46 (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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45B THR* 1.3 72.7 - - - +
47B THR* 1.3 60.1 + - - +
49B GLY* 3.8 0.3 - - - -
50B ASN* 2.7 37.0 + - - -
62B ALA* 4.4 3.7 - - - +
63B MET 2.9 23.3 + - - -
64B LEU 3.0 9.4 + - - -
65B SER* 3.7 1.5 - - - +
143E TYR* 3.8 15.5 - - - -
147E LEU* 4.1 4.0 - - - -
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Residues in contact with THR 47 (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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23B LYS* 3.7 15.0 - - - -
46B GLY* 1.3 68.3 - - - -
48B THR* 1.3 69.5 + - - +
49B GLY 3.0 0.3 + - - -
50B ASN* 3.1 3.6 + - - +
51B LEU* 3.0 33.6 + - + +
65B SER* 3.4 8.3 + - - -
202B PGA 2.9 29.7 + - - -
147E LEU* 4.1 13.3 - - - +
150E ARG* 3.5 35.2 + - + +
151E LEU* 4.1 18.6 - - + -
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Residues in contact with THR 48 (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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16B LEU 3.5 17.0 - - - +
18B ALA* 3.4 23.7 + - - +
23B LYS* 3.8 11.5 - - + +
26B LEU* 3.5 30.7 - - + -
27B MET* 6.0 1.1 - - - -
44B ALA* 4.2 0.9 - - + -
45B THR* 3.8 8.3 - - - -
47B THR* 1.3 74.6 - - - +
49B GLY* 1.3 63.7 + - - +
51B LEU* 3.4 5.0 + - - +
52B ILE* 3.2 31.7 + - + +
202B PGA 2.7 27.4 + - - -
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Residues in contact with GLY 49 (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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44B ALA* 3.5 18.1 - - - +
45B THR 2.8 21.4 + - - -
46B GLY 3.8 0.9 - - - -
47B THR 3.0 0.2 + - - -
48B THR* 1.3 73.3 - - - +
50B ASN* 1.3 63.0 + - - +
52B ILE* 3.2 5.2 + - - +
53B SER* 3.1 23.5 + - - -
60B VAL* 4.1 13.2 - - - +
62B ALA* 4.4 8.7 - - - -
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Residues in contact with ASN 50 (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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46B GLY* 2.7 27.9 + - - +
47B THR 3.1 1.6 + - - -
49B GLY* 1.3 75.5 - - - +
51B LEU* 1.3 64.0 + - - +
53B SER* 3.2 8.7 + - - -
54B ARG* 3.1 37.0 + - - +
62B ALA* 4.6 12.1 - - - +
147E LEU* 3.8 25.0 - - - +
151E LEU* 3.8 25.9 - - + +
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Residues in contact with LEU 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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23B LYS* 3.6 34.5 - - + -
27B MET* 3.9 17.4 - - + +
47B THR* 3.0 25.8 + - + +
48B THR* 3.8 4.9 - - - +
50B ASN* 1.3 76.1 - - - +
52B ILE* 1.3 58.3 + - - +
54B ARG* 3.9 10.1 - - - +
55B ALA* 3.2 28.8 + - - +
150E ARG 5.7 1.6 - - - +
151E LEU* 3.7 27.4 - - + +
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Residues in contact with ILE 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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16B LEU* 4.0 24.0 - - + -
26B LEU* 4.4 4.9 - - + -
27B MET* 3.6 25.6 - - + -
30B VAL* 4.2 28.0 - - + -
42B LEU* 5.3 2.2 - - + -
44B ALA* 5.2 1.6 - - + -
48B THR* 3.2 33.3 + - + +
49B GLY* 3.6 8.1 - - - +
50B ASN 3.2 0.6 - - - -
51B LEU* 1.3 74.5 - - - +
53B SER* 1.3 67.9 + - - +
54B ARG 3.1 1.3 - - - -
55B ALA 3.1 1.9 + - - -
56B THR* 2.9 39.3 + - + +
58B MET* 4.4 4.0 - - + -
60B VAL* 3.9 17.0 - - + -
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Residues in contact with SER 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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49B GLY 3.1 11.0 + - - -
50B ASN* 3.2 15.4 + - - -
52B ILE* 1.3 78.5 - - - +
54B ARG* 1.3 63.5 + - - +
56B THR* 4.2 2.5 - - - -
57B GLY* 2.7 30.3 + - - -
58B MET 3.2 24.9 - - - -
60B VAL* 4.2 12.3 - - - +
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Residues in contact with ARG 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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50B ASN* 3.1 24.5 + - + +
51B LEU* 3.9 10.3 - - + +
52B ILE 3.1 0.6 - - - -
53B SER* 1.3 86.9 + - - +
55B ALA* 1.3 61.1 + - - +
57B GLY* 4.3 2.1 + - - -
151E LEU* 3.5 52.3 + - - +
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Residues in contact with ALA 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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27B MET* 3.9 19.7 - - + -
31B GLU* 4.8 13.2 - - - +
51B LEU 3.2 15.7 + - - +
52B ILE 3.1 2.0 + - - -
54B ARG* 1.3 78.6 - - - +
56B THR* 1.3 62.1 + - + +
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Residues in contact with THR 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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27B MET* 4.8 2.9 - - + -
30B VAL* 4.6 4.3 - - + -
31B GLU* 4.2 21.3 - - + -
34B GLN* 3.2 40.8 + - - +
52B ILE* 2.9 26.3 + - + +
55B ALA* 1.3 85.8 - - + +
57B GLY* 1.3 62.4 + - - +
58B MET* 3.2 34.8 + - + +
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Residues in contact with GLY 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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53B SER 2.7 21.8 + - - -
54B ARG 4.3 2.0 + - - -
55B ALA 3.9 0.2 - - - -
56B THR* 1.3 72.7 + - - +
58B MET* 1.3 65.5 + - - +
59B ASN* 3.8 6.8 + - - +
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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