Contacts of the helix formed by residues 38 - 53 (chain C) in PDB entry 1SL0
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 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C SER 4.3 3.6 - - - +
34C TYR* 3.5 20.6 - - + -
35C ARG* 2.5 53.4 + - - +
37C SER* 1.3 75.9 - - - +
39C PHE* 1.3 52.7 + - - -
40C GLY 3.2 1.6 - - - -
41C ALA* 2.6 35.2 + - + +
42C TYR 2.7 11.7 + - - -
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Residues in contact with PHE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 6.5 0.2 - - + -
18C PHE* 3.1 34.5 - - + -
20C CYS* 6.2 2.2 - - - -
34C TYR* 5.3 0.4 - - - -
35C ARG 3.1 6.5 + - - +
36C PRO* 3.6 16.6 - - + +
37C SER 3.2 1.8 - - - +
38C ASP* 1.3 74.8 - - - +
40C GLY* 1.3 64.4 + - - +
42C TYR* 2.8 25.5 + + + +
43C LEU* 2.9 40.7 + - + +
69C LEU* 3.9 22.2 - - + -
72C LEU* 3.9 24.7 - - + -
73C ALA* 4.2 9.2 - - - -
76C GLN* 4.9 7.0 - - + +
77C LEU* 3.4 43.7 - - + -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER 4.3 4.0 + - - -
38C ASP 3.2 0.8 - - - -
39C PHE* 1.3 80.4 - - - +
41C ALA* 1.3 55.6 + - - +
43C LEU* 3.4 1.8 + - - -
44C ASP* 3.0 16.7 + - - +
77C LEU* 3.7 23.7 - - - +
79C ARG* 2.9 28.3 + - - -
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 3.5 18.7 - - + -
37C SER 5.2 0.2 + - - -
38C ASP* 2.6 27.1 + - + +
40C GLY* 1.3 69.0 - - - +
42C TYR* 1.3 52.8 + - - +
44C ASP* 2.8 12.8 + - - +
45C ALA* 2.8 32.4 + - - +
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER* 2.5 33.5 + - - -
5C ASP 3.4 2.3 + - - -
6C ILE* 2.8 34.7 - - + +
20C CYS 5.9 0.2 - - - -
21C GLY* 3.3 38.1 - - - +
22C VAL 3.8 1.3 - - - -
23C ILE* 4.2 5.6 - - + -
34C TYR* 3.1 30.4 - + + -
38C ASP 2.7 11.4 + - - +
39C PHE* 3.0 18.6 - + - +
41C ALA* 1.3 74.3 - - - +
43C LEU* 1.3 76.0 + - + +
45C ALA* 3.2 10.0 + - - +
46C LEU* 3.3 32.2 + - + +
58C PHE* 3.6 5.5 - - - -
69C LEU* 3.9 12.3 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PHE* 2.9 44.3 + - + +
40C GLY* 3.6 2.9 - - - +
42C TYR* 1.3 91.4 - - + +
44C ASP* 1.3 55.9 + - - +
46C LEU* 3.6 0.8 + - - -
47C GLU* 3.0 30.5 + - - +
69C LEU* 4.0 12.3 - - + -
73C ALA* 3.7 25.1 - - + -
77C LEU* 4.6 2.0 - - + -
79C ARG* 2.9 33.2 - - - +
81C PHE* 3.4 40.7 - - + -
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLY 3.0 17.5 + - - +
41C ALA* 2.8 15.3 + - - +
43C LEU* 1.3 77.9 - - - +
45C ALA* 1.3 55.6 + - - +
47C GLU* 3.3 12.5 + - - +
48C ALA* 2.9 28.6 + - - +
79C ARG* 3.7 16.2 + - - +
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 4.7 4.8 - - - +
23C ILE* 3.8 11.9 - - + -
34C TYR* 2.9 33.4 - - + +
41C ALA 2.8 9.7 + - - +
42C TYR 3.2 9.8 + - - +
44C ASP* 1.3 73.2 - - - +
46C LEU* 1.3 57.0 + - - +
48C ALA* 2.8 28.7 + - - +
49C GLU* 3.4 5.2 + - - +
52C ARG* 4.9 0.9 + - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ILE* 4.5 14.1 - - + -
4C SER* 4.2 7.4 - - - -
23C ILE* 3.4 28.9 - - + -
42C TYR* 3.3 46.8 + - + +
43C LEU 4.1 3.4 - - - +
45C ALA* 1.3 70.0 - - - +
47C GLU* 1.3 63.5 + - - +
48C ALA 2.8 6.8 + - - -
49C GLU* 3.1 16.4 + - - +
50C VAL* 3.4 15.6 + - - +
56C ILE* 3.8 19.9 - - + +
58C PHE* 4.0 19.3 - - + -
69C LEU* 4.3 8.3 - - + -
81C PHE* 4.5 10.8 - - + -
83C LEU* 4.7 3.4 - - + -
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 3.0 16.6 + - - +
44C ASP* 3.6 13.0 - - - +
46C LEU* 1.3 76.2 - - - +
48C ALA* 1.3 59.9 + - - +
50C VAL* 3.6 14.0 - - + +
51C ALA* 3.5 16.6 + - - +
79C ARG* 3.5 24.4 + - - -
80C GLU 4.9 1.6 - - - +
81C PHE* 3.6 22.5 - - + -
82C HIS 5.3 0.9 + - - -
83C LEU* 5.1 3.1 - - + -
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP 2.9 12.1 + - - +
45C ALA* 2.8 20.0 - - - +
46C LEU 2.8 1.6 - - - -
47C GLU* 1.3 76.1 - - - +
49C GLU* 1.3 58.2 + - - +
50C VAL 3.2 1.3 - - - -
51C ALA* 2.9 28.0 + - - +
52C ARG* 3.1 23.9 + - - +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.0 23.3 + - - +
2C ILE* 3.0 44.8 - - + +
25C ASP* 4.1 4.7 - - - +
45C ALA 3.4 2.2 + - - -
46C LEU 3.1 8.1 + - - +
48C ALA* 1.3 77.4 - - - +
50C VAL* 1.3 55.4 + - - +
52C ARG* 2.8 41.7 + - - +
53C GLY 2.8 9.4 + - - -
54C GLY* 2.7 44.3 + - - -
55C LEU 3.8 10.3 - - - +
56C ILE* 4.2 7.9 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU 3.4 15.7 - - - +
47C GLU* 3.6 13.5 - - + +
48C ALA 3.2 0.2 - - - -
49C GLU* 1.3 76.8 - - - +
51C ALA* 1.3 61.1 + - - +
53C GLY* 3.2 12.3 + - - -
56C ILE* 3.9 7.2 - - + -
83C LEU* 3.4 28.0 - - + -
84C PRO* 4.0 26.2 - - + -
87C ASN* 3.9 17.4 + - - +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU 3.5 9.0 + - - +
48C ALA* 2.9 16.4 + - - +
50C VAL* 1.3 78.1 - - - +
52C ARG* 1.3 62.6 + - + +
53C GLY* 3.0 2.7 + - - -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 6.0 0.2 - - - +
25C ASP* 4.2 15.5 + - - -
27C SER* 4.9 7.9 + - - -
28C THR* 6.1 0.4 - - - +
45C ALA 4.9 0.4 + - - -
48C ALA* 3.5 30.6 + - - +
49C GLU* 2.8 44.4 + - - +
51C ALA* 1.3 78.2 - - - +
53C GLY* 1.3 61.7 + - - +
54C GLY* 3.9 5.6 - - - +
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Residues in contact with GLY 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU 2.8 2.2 + - - -
50C VAL 3.2 11.0 + - - -
51C ALA 3.0 4.4 - - - -
52C ARG* 1.3 82.4 - - - +
54C GLY* 1.3 64.6 + - - +
87C ASN* 4.1 6.5 - - - -
202C GLY* 3.7 7.4 - - - -
203C TYR* 3.6 32.2 + - - -
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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