Contacts of the helix formed by residues 46 - 60 (chain C) in PDB entry 3D5K
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 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C PHE 3.5 1.1 - - - +
45C ARG* 1.3 76.2 - - - +
47C PRO* 1.4 60.5 - - - +
48C GLN* 3.0 16.1 + - - +
49C LEU* 3.3 19.0 + - + +
50C GLN* 3.1 28.6 + - - +
165C TYR* 2.7 32.3 + - + -
169C LYS* 3.8 3.3 + - - +
249C GLY* 3.3 14.9 - - - -
250C LEU* 3.2 34.0 + - + +
256C LEU* 4.0 13.5 + - + +
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Residues in contact with PRO 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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45C ARG 3.2 10.7 - - - +
46C ASP* 1.4 86.9 - - - +
48C GLN* 1.3 61.4 + - - +
50C GLN* 3.6 18.6 + - + +
51C GLN* 3.3 20.6 + - - +
247C PRO* 4.1 19.5 - - + +
248C GLN 3.5 21.3 - - - +
250C LEU* 4.3 12.3 - - + -
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Residues in contact with GLN 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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46C ASP* 3.0 11.9 + - - +
47C PRO* 1.3 77.1 - - - +
49C LEU* 1.3 64.2 + - - +
51C GLN* 3.5 3.6 + - - +
52C LEU* 3.1 26.0 + - + +
165C TYR* 3.4 30.5 + - + +
169C LYS* 4.9 2.6 - - - +
246C LEU* 3.9 34.6 - - + +
247C PRO* 3.0 35.2 + - - +
248C GLN* 4.7 0.2 - - - -
249C GLY* 3.7 12.1 + - - -
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Residues in contact with LEU 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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44C PHE* 3.6 33.7 - - + -
46C ASP* 3.3 18.7 + - + +
48C GLN* 1.3 77.7 - - - +
50C GLN* 1.3 59.4 + - - +
52C LEU* 3.1 7.0 + - + -
53C ILE* 2.8 52.4 + - + +
161C VAL* 4.3 7.0 - - + +
162C ALA* 4.0 19.7 - - + +
165C TYR* 3.7 48.6 + - + -
166C LEU* 5.2 7.4 - - + -
257C LEU* 5.6 2.0 - - + -
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 3.3 21.4 - - + +
41C ARG* 3.1 60.6 + - - +
44C PHE* 2.6 33.6 + - + +
45C ARG* 3.9 13.1 + - - +
46C ASP 3.1 14.1 + - - +
47C PRO* 3.7 17.6 - - - +
48C GLN 3.3 0.2 - - - -
49C LEU* 1.3 75.3 - - - +
51C GLN* 1.3 60.5 + - - +
53C ILE* 4.7 2.2 - - - -
54C GLY* 3.3 14.9 + - - -
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Residues in contact with GLN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ARG* 4.6 3.8 - - - +
47C PRO 3.3 10.3 + - - +
48C GLN 3.8 7.4 - - - +
49C LEU 3.2 0.6 - - - -
50C GLN* 1.3 77.2 - - - +
52C LEU* 1.3 66.0 + - - +
54C GLY* 3.1 3.6 + - - -
55C VAL* 3.0 31.2 + - + +
243C PRO* 4.0 13.7 - - - +
245C ASN* 3.8 14.1 + - - +
246C LEU* 3.7 26.3 - - + +
247C PRO* 3.6 18.4 - - + +
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 3.1 29.0 + - + +
49C LEU* 3.1 8.4 + - + +
51C GLN* 1.3 76.7 - - - +
53C ILE* 1.3 61.6 + - - +
55C VAL* 3.2 5.1 + - - +
56C ALA* 3.0 18.7 + - - +
161C VAL* 4.4 9.0 - - + -
165C TYR* 3.4 38.4 - - + -
234C LEU* 4.6 13.5 - - + -
238C LEU* 3.3 43.6 - - + +
242C ILE* 4.9 7.9 - - + -
243C PRO* 4.2 18.2 - - + -
246C LEU* 4.6 8.1 - - + -
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Residues in contact with ILE 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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40C TRP* 3.7 33.4 - - + -
44C PHE* 3.5 40.6 - - + -
49C LEU* 2.8 44.6 + - + +
50C GLN 3.9 4.9 - - - +
52C LEU* 1.3 72.1 - - - +
54C GLY* 1.3 56.9 + - - +
56C ALA* 3.4 4.7 + - - +
57C LEU* 2.9 29.8 + - + +
158C VAL* 4.0 26.0 - - + +
161C VAL* 4.0 17.5 - - + -
162C ALA* 5.1 0.2 - - + -
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Residues in contact with GLY 54 (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 TRP* 4.2 10.5 - - - -
41C ARG* 5.7 2.7 - - - -
50C GLN 3.3 9.2 + - - -
51C GLN* 3.1 8.2 + - - -
53C ILE* 1.3 77.4 - - - +
55C VAL* 1.3 64.0 + - - +
57C LEU* 3.5 14.8 + - - +
58C GLU* 3.6 17.7 + - - +
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Residues in contact with VAL 55 (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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51C GLN* 3.0 24.2 + - + +
52C LEU* 3.5 9.4 - - - +
54C GLY* 1.3 75.3 - - - +
56C ALA* 1.3 57.9 - - - +
58C GLU* 3.2 2.8 + - - +
59C ASN* 2.8 40.8 + - - +
238C LEU* 4.2 17.0 - - + +
240C SER* 3.6 24.0 - - - +
241C GLY 4.8 6.1 - - - +
243C PRO* 3.9 25.1 - - + -
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Residues in contact with ALA 56 (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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52C LEU 3.0 15.8 + - - +
53C ILE* 3.6 5.8 - - - +
54C GLY 3.3 0.2 - - - -
55C VAL* 1.3 73.7 - - - +
57C LEU* 1.3 59.5 + - - +
58C GLU 3.0 5.2 - - - -
60C ASN* 3.1 29.3 + - - +
63C LEU* 4.7 0.3 - - - +
157C LEU* 3.4 10.5 - - + +
161C VAL* 3.7 28.9 - - + -
237C LEU 3.8 10.8 - - - +
238C LEU* 3.7 15.9 - - + +
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Residues in contact with LEU 57 (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 TRP* 3.5 39.0 - - + +
53C ILE* 2.9 23.6 + - + +
54C GLY* 3.9 8.7 - - - +
55C VAL 3.3 0.6 - - - -
56C ALA* 1.3 75.9 - - - +
58C GLU* 1.3 58.4 + - - +
60C ASN 6.0 0.2 - - - -
63C LEU* 3.9 25.2 - - + +
154C GLN* 3.6 38.8 - - + +
157C LEU* 4.5 7.4 - - + -
158C VAL* 4.4 11.2 - - + -
452C GLN* 6.0 1.3 - - + +
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Residues in contact with GLU 58 (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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54C GLY 3.6 11.4 + - - +
55C VAL* 3.2 4.3 + - - +
56C ALA 3.0 0.4 - - - -
57C LEU* 1.3 81.3 - - - +
59C ASN* 1.3 65.5 + - - +
60C ASN 3.8 1.6 - - - -
64C ARG* 2.7 33.1 + - - +
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Residues in contact with ASN 59 (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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55C VAL* 2.8 27.0 + - - +
58C GLU* 1.3 89.7 - - - +
60C ASN* 1.3 65.9 + - - +
61C ARG* 2.7 30.5 + - - +
64C ARG* 3.6 12.2 - - - +
238C LEU 3.0 19.1 - - - +
239C GLY* 3.6 13.6 + - - +
240C SER* 4.1 16.3 + - - +
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Residues in contact with ASN 60 (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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360A LYS* 6.4 0.2 - - - +
56C ALA 3.1 20.7 + - - +
57C LEU 6.0 0.2 - - - -
58C GLU 3.8 1.4 - - - +
59C ASN* 1.3 76.0 - - - +
61C ARG* 1.3 63.0 + - - +
62C ASP* 2.8 19.4 + - - +
63C LEU* 2.8 33.8 + - + +
64C ARG* 3.3 19.8 + - - +
157C LEU* 3.4 26.1 - - + +
236C LEU 4.5 3.6 + - - -
237C LEU* 3.2 34.1 + - - +
238C LEU 3.4 5.8 + - - -
239C GLY* 4.4 3.8 - - - -
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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