Contacts of the helix formed by residues 39 - 52 (chain C) in PDB entry 3R2W
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 HIS 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C GLU* 3.9 30.7 - - + +
37C PHE 3.2 0.2 - - - -
38C GLU* 1.3 82.9 + - - +
40C THR* 1.3 67.5 + - - +
41C LYS 3.7 0.9 - - - -
42C LYS* 4.1 11.9 - - - +
43C ASP* 3.6 19.3 + - - +
178C ASN* 6.3 1.1 - - - -
180C SER* 5.3 3.1 - - - -
221C ASN* 5.2 11.8 + - - +
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Residues in contact with THR 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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29C LEU* 4.5 13.7 - - + -
36C GLU* 4.0 22.6 + - - +
37C PHE* 3.8 3.4 + - - -
39C HIS* 1.3 87.1 + - - +
41C LYS* 1.3 59.4 + - - +
42C LYS 3.1 4.9 - - - -
43C ASP* 4.1 4.0 - - + +
44C LEU* 3.1 52.7 + - + +
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Residues in contact with LYS 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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29C LEU* 3.7 18.2 - - + -
37C PHE* 3.5 50.8 + - + +
38C GLU 5.8 0.4 - - - -
40C THR* 1.3 76.2 - - - +
42C LYS* 1.3 55.8 + - - +
44C LEU* 4.4 4.1 - - - +
45C ASP* 3.5 24.5 + - - +
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Residues in contact with LYS 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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38C GLU 4.6 5.6 - - - +
39C HIS* 4.4 16.5 - - - +
40C THR 3.1 1.4 - - - +
41C LYS* 1.3 79.6 - - - +
43C ASP* 1.3 62.7 + - - +
44C LEU 3.5 0.2 - - - -
45C ASP* 3.8 4.3 + - - +
46C GLY* 3.4 15.2 + - - -
221C ASN* 3.9 21.8 - - - +
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Residues in contact with ASP 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 HIS 3.6 16.5 + - - +
40C THR* 3.4 7.0 + - + +
42C LYS* 1.3 76.9 - - - +
44C LEU* 1.3 63.3 + - + +
46C GLY* 2.9 20.1 + - - -
47C PHE* 3.4 5.9 + - - +
180C SER* 3.6 30.7 - - - -
181C ARG* 4.1 14.8 - - + +
182C TYR* 4.1 11.2 + - + -
221C ASN* 5.4 2.4 - - - +
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Residues in contact with LEU 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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25C LEU* 3.5 51.5 - - + +
28C ILE* 4.5 12.8 - - + -
29C LEU* 3.8 26.0 - - + -
40C THR* 3.1 33.5 + - + +
41C LYS* 4.7 3.4 - - - +
43C ASP* 1.3 80.0 - - + +
45C ASP* 1.3 57.2 + - - +
47C PHE* 3.3 24.5 + - - +
48C ARG* 3.7 4.7 + - - +
181C ARG 5.9 1.8 - - - +
182C TYR* 6.5 0.2 - - - -
183C PRO* 5.0 18.6 - - + -
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Residues in contact with ASP 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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41C LYS 3.5 19.4 + - - +
42C LYS* 3.9 5.2 - - - +
43C ASP 3.2 0.6 - - - -
44C LEU* 1.3 75.5 - - - +
46C GLY* 1.3 61.1 + - - +
48C ARG* 4.2 13.4 + - + +
49C LYS* 4.3 8.5 + - - +
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Residues in contact with GLY 46 (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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42C LYS 3.4 8.7 + - - -
43C ASP* 2.9 11.8 + - - -
45C ASP* 1.3 77.6 - - - +
47C PHE* 1.3 62.6 + - - +
48C ARG 3.3 0.4 - - - -
49C LYS* 3.3 21.0 + - - +
50C LEU* 3.7 10.2 + - - +
182C TYR* 3.7 13.0 - - - -
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Residues in contact with PHE 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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21C VAL* 4.9 16.4 - - + -
25C LEU* 5.0 13.0 - - + -
43C ASP 3.4 4.7 + - - +
44C LEU* 3.3 15.2 + - + +
46C GLY* 1.3 76.5 - - - +
48C ARG* 1.3 52.2 + - - +
50C LEU* 3.1 7.2 + - + +
51C PHE* 2.8 50.4 + - + +
182C TYR* 3.4 33.3 + + + -
183C PRO* 3.9 35.0 - - + -
185C ILE* 4.8 16.6 - - + -
208C TYR* 4.2 7.0 - - - -
357C LEU* 3.9 28.0 - - + -
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Residues in contact with ARG 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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18C GLU* 3.0 56.0 + - - +
19C LEU* 5.0 3.4 - - - +
21C VAL* 5.1 4.9 - - - +
22C LYS* 3.1 28.2 - - - +
25C LEU* 4.2 18.4 - - + +
44C LEU 3.7 7.1 + - - +
45C ASP* 4.3 12.6 - - - +
46C GLY 3.3 0.6 - - - -
47C PHE* 1.3 75.1 - - - +
49C LYS* 1.3 64.8 + - - +
50C LEU 3.1 2.3 + - - -
51C PHE* 4.4 9.9 - - - +
52C HIS* 3.3 25.3 + - + +
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Residues in contact with LYS 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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45C ASP 4.3 5.9 + - - +
46C GLY* 3.3 14.7 + - - +
48C ARG* 1.3 77.6 - - - +
50C LEU* 1.3 64.1 + - + +
52C HIS* 4.5 4.3 - - - +
53C ARG* 3.7 16.1 + - - +
335C ASN* 5.2 9.0 - - - +
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Residues in contact with LEU 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 GLY 3.7 9.6 - - - +
47C PHE* 3.1 7.6 + - + +
48C ARG 3.1 0.4 - - - -
49C LYS* 1.3 81.8 - - + +
51C PHE* 1.3 60.8 + - - +
52C HIS 3.2 1.8 - - - -
53C ARG* 3.0 18.4 + - - +
54C PHE* 3.1 11.3 + - - +
182C TYR* 4.0 35.0 - - + +
210C PRO* 6.2 1.6 - - + -
339C MET 5.6 0.4 - - - +
341C ILE* 3.8 35.6 - - + +
357C LEU* 4.7 28.2 - - + +
358C GLU* 5.9 1.3 - - - +
359C THR* 4.3 14.4 - - + -
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 4.5 12.9 - - + +
21C VAL* 5.9 3.4 - - + -
47C PHE* 2.8 44.1 + - + +
48C ARG* 4.4 10.8 - - - +
50C LEU* 1.3 72.7 - - - +
52C HIS* 1.3 57.4 + - - +
54C PHE* 3.2 23.6 - - - +
55C LEU 4.3 2.4 + - - -
357C LEU* 5.1 4.5 - - + +
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Residues in contact with HIS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.4 30.4 + - - +
48C ARG* 3.3 19.0 + - + +
49C LYS* 4.7 3.8 - - - +
50C LEU 3.2 0.6 - - - -
51C PHE* 1.3 75.4 - - - +
53C ARG* 1.3 58.9 + - - +
54C PHE 3.2 3.0 + - - -
55C LEU 4.6 1.8 + - - -
56C GLN* 3.7 18.1 + - + +
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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