Contacts of the helix formed by residues 47 - 60 (chain C) in PDB entry 2PK9
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 PRO 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.6 28.7 - - + -
39C LYS* 4.3 15.9 - - + +
45C GLY 3.4 8.7 - - - +
46C THR* 1.4 90.0 - - + +
48C SER* 1.3 65.8 + - - +
49C THR* 4.2 8.5 - - - +
50C ALA* 3.2 15.1 + - + +
51C ILE* 3.2 19.6 + - - +
78C LEU* 4.7 2.2 - - + -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR 3.4 2.8 + - - -
47C PRO* 1.3 71.4 - - - +
49C THR* 1.3 60.4 + - - +
51C ILE* 3.3 12.9 + - - +
52C ARG* 3.0 33.6 + - - +
132D LYS* 2.9 37.6 + - - +
138D PHE* 3.5 40.6 - - - -
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Residues in contact with THR 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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38C VAL* 5.9 0.9 - - - +
47C PRO* 4.2 9.4 - - - +
48C SER* 1.3 80.3 - - - +
50C ALA* 1.3 54.0 + - - +
52C ARG* 3.6 3.7 - - - +
53C GLU* 2.6 41.4 + - - +
153C GLY* 3.5 31.6 - - - +
154C LEU* 4.4 12.1 - - + -
138D PHE* 6.2 2.5 - - + -
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Residues in contact with ALA 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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38C VAL* 4.1 15.5 - - + -
46C THR* 4.4 0.9 - - + -
47C PRO* 3.2 21.6 + - + +
49C THR* 1.3 80.4 + - - +
51C ILE* 1.3 62.8 + - - +
53C GLU* 4.5 5.6 - - - -
54C ILE* 2.9 35.4 + - + +
78C LEU* 3.8 29.4 - - + -
80C LEU* 5.3 4.9 - - + -
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.6 24.2 - - + +
47C PRO 3.2 15.8 + - - +
48C SER* 3.3 8.3 + - - +
50C ALA* 1.3 76.2 - - - +
52C ARG* 1.3 57.1 + - - +
54C ILE* 4.3 0.9 - - - +
55C SER* 3.0 27.7 + - - -
129D VAL* 4.6 6.5 - - + -
132D LYS* 3.9 18.4 - - + +
133D GLY* 4.1 9.4 - - - -
159D GLU* 3.3 26.5 - - - +
163D LEU* 3.8 26.2 - - + -
168D TYR* 4.2 10.0 - - + -
170D ILE* 3.8 21.0 - - + +
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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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48C SER* 3.0 21.5 + - - +
49C THR* 3.6 4.9 - - - +
51C ILE* 1.3 77.8 - - - +
53C GLU* 1.3 59.9 + - - +
54C ILE 3.3 0.2 - - - -
55C SER* 4.4 3.6 - - - -
56C LEU* 2.9 50.9 + - + +
132C ARG* 5.7 0.9 - - - +
152C PHE 4.4 1.6 - - - +
153C GLY 3.5 21.1 - - - +
154C LEU* 4.8 0.9 - - - +
155C ALA 3.0 19.2 + - - +
156C ARG* 3.1 31.3 - - - +
157C ALA 4.6 1.2 - - - +
132D LYS 4.1 4.9 + - - -
133D GLY 3.6 19.5 + - - +
134D LEU* 3.3 9.3 - - - +
135D CYS 2.8 45.6 + - - +
136D ASP* 5.3 1.1 - - - -
138D PHE* 6.2 0.6 - - - -
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Residues in contact with GLU 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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36C LYS* 2.8 36.2 + - - -
38C VAL* 6.0 0.3 - - - +
49C THR* 2.6 25.3 + - - +
50C ALA* 4.0 4.1 - - - +
52C ARG* 1.3 73.8 - - - +
54C ILE* 1.3 58.7 + - - +
56C LEU* 4.4 1.5 - - - +
57C MET* 2.8 38.4 + - + +
68C LEU* 5.3 0.2 - - - -
80C LEU* 3.9 12.5 - - + +
82C PHE* 4.4 18.3 - - + -
151C ASP* 3.5 6.9 - - - +
152C PHE* 3.2 34.7 + - + +
153C GLY* 3.2 18.4 + - - +
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Residues in contact with ILE 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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50C ALA 2.9 20.2 + - - +
53C GLU* 1.3 79.1 - - - +
55C SER* 1.3 64.6 + - - +
56C LEU 3.3 0.5 + - - -
57C MET* 3.4 9.2 + - - +
58C LYS* 3.5 27.1 + - - +
68C LEU* 4.1 9.9 - - + +
71C VAL* 3.8 23.3 - - + -
78C LEU* 4.4 4.7 - - + -
80C LEU* 3.6 34.1 - - + -
168D TYR* 3.4 61.9 - - + +
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Residues in contact with SER 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 ILE 3.0 20.8 + - - -
52C ARG* 3.4 5.3 + - - -
54C ILE* 1.3 81.0 - - - +
56C LEU* 1.3 63.6 + - - +
58C LYS* 3.7 15.8 + - - +
59C GLU* 4.0 4.9 + - - +
133D GLY 4.7 1.9 + - - -
168D TYR 3.4 25.7 - - - +
169D ARG* 6.0 0.3 - - - -
170D ILE* 3.7 13.6 - - - +
171D ILE* 3.1 32.1 - - - +
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Residues in contact with LEU 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 ARG* 2.9 42.7 + - + +
53C GLU* 4.4 2.2 - - - +
55C SER* 1.3 76.8 + - - +
57C MET* 1.3 74.5 + - + +
59C GLU* 3.1 16.9 + - - +
60C LEU* 3.4 17.7 + - + +
129C ILE* 3.9 32.9 - - + +
152C PHE* 3.9 6.7 - - + +
155C ALA* 3.7 35.0 - - + +
156C ARG* 4.0 1.6 - - - +
157C ALA* 3.9 12.8 - - + +
171D ILE* 3.8 19.5 - - + -
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Residues in contact with MET 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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53C GLU* 2.8 26.7 - - + +
54C ILE 3.4 5.1 + - - +
56C LEU* 1.3 76.2 - - - +
58C LYS* 1.3 57.5 + - - +
60C LEU* 2.9 39.5 + - + +
61C LYS* 3.7 7.0 - - - -
65C ILE* 4.3 7.9 - - + -
66C VAL* 4.1 18.6 - - - +
68C LEU* 4.0 30.1 - - + +
82C PHE* 4.2 20.4 - - + -
150C GLY* 6.2 0.7 - - - -
151C ASP 6.0 1.1 - - - -
152C PHE* 3.4 51.4 - - + -
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Residues in contact with LYS 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 ILE* 3.6 29.8 - - - +
55C SER 3.8 9.0 - - - +
56C LEU 3.2 0.6 - - - -
57C MET* 1.3 76.2 - - + +
59C GLU* 1.3 58.5 + - + +
61C LYS* 3.2 30.1 + - - +
68C LEU* 5.1 8.8 - - + +
70C ASP* 6.0 2.6 + - - +
71C VAL* 5.4 4.9 - - - +
167D ASN* 3.2 31.8 - - - +
168D TYR* 4.6 4.3 - - - +
169D ARG* 3.7 34.4 + - + +
183D GLU* 3.7 26.8 + - - +
204D TYR* 3.8 7.4 + - - +
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Residues in contact with GLU 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 SER 4.2 11.9 - - - +
56C LEU 3.1 9.2 + - - +
58C LYS* 1.3 78.4 - - + +
60C LEU* 1.3 59.7 + - - +
61C LYS* 3.7 4.2 + - - -
123C PHE* 4.0 5.5 - - - -
127C ASN* 3.8 15.2 - - - +
129C ILE* 4.2 14.4 - - + -
169D ARG* 3.3 30.4 + - - -
171D ILE* 4.4 21.3 - - + +
173D ARG* 3.0 41.7 + - - +
176D ASN* 4.0 5.9 - - - +
179D LEU* 5.3 1.4 - - - +
204D TYR* 5.5 4.0 - - - -
206D TYR* 3.8 13.0 + - - -
214D TYR* 5.7 0.4 - - - +
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Residues in contact with LEU 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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56C LEU* 3.4 14.3 + - + +
57C MET* 2.9 27.4 + - + +
59C GLU* 1.3 77.8 - - - +
61C LYS* 1.3 59.8 + - - +
62C HIS 3.8 2.9 + - - -
65C ILE* 3.8 26.0 - - + +
66C VAL 4.9 3.3 - - - +
67C ARG* 5.6 2.4 - - - +
123C PHE* 3.6 26.9 - - + -
124C CYS* 3.8 24.0 - - - -
127C ASN* 4.4 3.6 - - + -
129C ILE* 4.0 27.6 - - + -
152C PHE* 3.7 35.9 - - + -
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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