Contacts of the helix formed by residues 46 - 62 (chain C) in PDB entry 3RCY
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 GLY 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP* 2.9 20.4 + - - -
60A ARG* 3.8 4.5 - - - -
22C TYR* 4.1 0.9 - - - -
45C VAL* 1.3 76.5 - - - +
47C PRO* 1.3 72.3 - - - +
48C GLU 3.3 2.7 - - - -
49C ALA* 3.2 4.5 + - - +
50C MET* 3.0 25.7 + - - +
384C LEU* 3.5 15.6 - - - +
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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
----------------------------------------------------------
60A ARG* 5.3 0.9 - - - +
10C VAL* 3.9 27.8 - - + +
22C TYR* 3.6 40.8 - - + +
24C ILE* 5.0 2.4 - - + +
46C GLY* 1.3 83.7 - - - +
48C GLU* 1.3 67.7 + - + +
50C MET* 3.2 7.8 + - + +
51C ARG* 2.9 31.9 + - - +
379C TYR* 3.8 20.2 - - + +
383C GLY 4.6 5.4 - - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 4.9 2.0 - - - +
46C GLY 3.3 1.0 - - - -
47C PRO* 1.3 82.3 - - + +
49C ALA* 1.3 62.9 + - - +
51C ARG* 3.2 53.0 + - - +
52C ALA* 3.5 7.6 + - - +
379C TYR 5.3 4.5 - - - +
380C HIS* 5.7 4.6 + - - -
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Residues in contact with ALA 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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52A ALA* 3.8 39.0 - - + +
53A VAL* 4.2 3.1 - - + +
56A ASP* 4.3 7.8 + - + +
45C VAL* 3.6 27.6 - - + -
46C GLY 3.2 4.7 + - - +
48C GLU* 1.3 77.7 - - - +
50C MET* 1.3 63.2 + - - +
52C ALA* 3.3 6.1 + - - +
53C VAL* 3.1 26.5 + - - +
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Residues in contact with MET 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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24C ILE* 4.1 18.6 - - + -
40C CYS* 5.6 0.9 - - + -
42C ALA* 3.6 44.2 - - + +
44C SER 5.8 0.2 - - - -
45C VAL* 3.8 18.6 - - - +
46C GLY 3.0 17.6 + - - +
47C PRO 3.2 7.4 + - - +
49C ALA* 1.3 73.9 - - - +
51C ARG* 1.3 59.2 + - - +
53C VAL* 3.2 13.0 + - + +
54C ILE* 2.8 52.1 + - + +
89C THR* 3.8 35.7 - - - +
93C ALA* 4.4 4.7 - - + +
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Residues in contact with ARG 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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8C ILE* 3.0 56.8 + - + +
9C ILE* 5.2 0.2 - - - +
10C VAL* 3.7 31.2 + - + +
24C ILE* 6.2 0.2 - - - +
47C PRO 2.9 16.4 + - - +
48C GLU* 3.2 43.4 + - - +
49C ALA 3.3 0.2 - - - -
50C MET* 1.3 75.8 - - - +
52C ALA* 1.3 56.3 + - - +
54C ILE* 4.5 1.5 - - - +
55C GLU* 2.9 38.4 + - + +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU 5.0 2.0 - - - +
49A ALA* 3.8 24.0 - - - +
52A ALA* 4.2 12.8 - - + -
48C GLU 3.5 7.2 + - - +
49C ALA 3.3 9.9 + - - +
51C ARG* 1.3 77.0 - - - +
53C VAL* 1.3 63.6 + - - +
55C GLU* 3.6 7.0 + - - +
56C ASP* 3.1 23.7 + - - +
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Residues in contact with VAL 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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45A VAL* 4.0 25.4 - - + -
49A ALA* 4.3 7.4 - - + -
53A VAL* 4.0 20.4 - - + -
49C ALA 3.1 19.6 + - - +
50C MET* 3.6 12.3 - - + +
52C ALA* 1.3 75.5 - - - +
54C ILE* 1.3 57.4 + - - +
56C ASP* 3.2 3.6 + - - +
57C VAL* 3.0 28.6 + - + +
89C THR* 3.9 34.1 - - + +
90C ALA* 4.4 4.3 - - - -
93C ALA* 3.8 19.1 - - + -
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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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6C LEU* 4.2 2.7 - - + -
8C ILE* 3.8 24.2 - - + -
24C ILE* 3.7 30.3 - - + -
26C VAL* 4.0 8.5 - - + -
40C CYS* 3.9 10.8 - - + -
50C MET* 2.8 39.4 + - + +
51C ARG 4.5 0.4 - - - +
53C VAL* 1.3 71.4 - - - +
55C GLU* 1.3 58.4 + - - +
57C VAL* 3.4 1.2 + - - +
58C PHE* 2.9 29.3 + - - +
93C ALA* 3.7 26.9 - - + +
97C LEU* 3.9 30.2 - - + +
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Residues in contact with GLU 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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6C LEU* 3.7 27.6 - - - +
7C ASP* 6.1 0.2 - - - -
8C ILE* 3.9 14.0 + - + +
51C ARG* 2.9 28.7 + - + +
52C ALA* 3.8 7.4 - - - +
54C ILE* 1.3 76.2 - - - +
56C ASP* 1.3 57.3 + - - +
58C PHE* 4.0 2.8 - - - +
59C ALA* 3.0 32.9 + - - +
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Residues in contact with ASP 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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44A SER 4.5 0.9 - - - +
45A VAL* 3.7 19.0 - - + +
46A GLY* 2.7 30.8 + - - -
49A ALA* 4.3 5.9 + - + +
52C ALA 3.1 15.0 + - - +
53C VAL 3.2 8.5 + - - +
55C GLU* 1.3 74.4 - - - +
57C VAL* 1.3 61.2 + - - +
59C ALA* 4.1 2.4 - - - +
60C ARG* 2.8 68.4 + - - +
61C HIS* 5.2 0.3 + - - -
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Residues in contact with VAL 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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44A SER 5.4 1.3 - - - +
45A VAL* 4.0 18.2 - - + -
53C VAL* 3.0 22.8 + - + +
54C ILE 3.9 3.4 - - - +
56C ASP* 1.3 75.4 - - - +
58C PHE* 1.3 64.8 + - - +
61C HIS* 3.1 31.7 + - + +
62C MET* 3.9 3.8 + - - +
77C VAL* 3.8 35.9 - - + -
90C ALA* 4.1 10.1 - - + +
93C ALA* 4.0 15.7 - - + -
94C PHE* 4.1 10.3 - - - +
97C LEU* 3.9 15.5 - - + -
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Residues in contact with PHE 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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3C LEU* 4.1 18.8 - - + -
4C ARG 3.8 28.7 - - - -
5C ASP* 4.1 7.6 - - - -
6C LEU* 3.8 32.1 - - + -
28C LEU* 3.6 24.7 - - + -
54C ILE 2.9 18.4 + - - +
55C GLU* 4.0 3.6 - - - +
57C VAL* 1.3 77.7 - - - +
59C ALA* 1.3 58.9 + - + +
62C MET* 2.9 24.6 + - + -
63C GLU* 2.8 60.7 + - + -
97C LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 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 GLU* 3.0 19.4 + - - +
56C ASP* 4.1 2.7 - - - +
58C PHE* 1.3 81.6 - - + +
60C ARG* 1.3 60.7 + - - +
63C GLU* 4.0 25.0 + - + +
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Residues in contact with ARG 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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46A GLY* 3.7 13.9 - - - -
47A PRO* 5.4 0.6 - - - +
382A THR 2.8 31.3 + - - -
383A GLY* 3.9 4.0 + - - -
384A LEU* 3.5 37.4 - - - +
387A GLU* 4.7 2.6 + - - -
56C ASP* 2.8 54.6 + - - +
59C ALA* 1.3 79.4 - - - +
61C HIS* 1.3 88.1 + - + +
62C MET 3.8 0.2 - - - -
76C ARG* 5.5 0.7 - - - -
80C SER* 4.3 0.4 - - - -
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Residues in contact with HIS 61 (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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44A SER 4.5 1.2 + - - -
384A LEU* 5.0 1.8 - - + -
56C ASP* 5.4 0.2 - - - -
57C VAL* 3.1 24.3 + - + +
60C ARG* 1.3 104.8 + - + +
62C MET* 1.3 64.6 + - + +
63C GLU 5.2 0.9 - - - -
73C MET* 3.9 5.0 - - - +
76C ARG* 3.0 61.0 + - + +
77C VAL* 3.8 32.8 - - + -
80C SER* 2.8 38.4 + - - -
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Residues in contact with MET 62 (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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3C LEU* 3.5 14.8 - - + +
28C LEU* 4.9 1.8 - - + -
57C VAL* 4.2 7.9 - - - +
58C PHE* 2.9 17.5 + - + +
60C ARG 3.8 0.4 - - - -
61C HIS* 1.3 89.1 - - + +
63C GLU* 1.3 70.0 + - - +
64C GLY 3.3 0.2 + - - -
65C GLU* 3.0 20.5 + - - +
73C MET* 3.7 31.6 - - + -
94C PHE* 3.8 28.0 - - + -
97C LEU* 3.6 47.6 - - + +
98C GLU* 4.2 0.4 - - - +
101C CYS* 3.8 21.5 - - - -
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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