Contacts of the helix formed by residues 37 - 51 (chain C) in PDB entry 2IT0
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 SER 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN* 1.3 76.3 - - - +
38C GLY* 1.3 66.7 + - - +
39C PRO* 3.3 1.3 - - - +
40C THR* 2.7 34.8 + - - -
41C VAL* 3.3 10.9 + - - +
16E C 2.9 18.1 + - - -
17E T 3.3 42.9 - - - +
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Residues in contact with GLY 38 (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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31C ALA* 4.6 8.9 - - - +
36C GLN 3.7 1.4 + - - -
37C SER* 1.3 69.8 - - - +
39C PRO* 1.3 70.2 - - - +
41C VAL* 3.1 29.5 + - - +
42C SER* 3.2 7.7 + - - -
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Residues in contact with PRO 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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37C SER* 3.3 11.4 - - - +
38C GLY* 1.3 90.5 - - - +
40C THR* 1.3 59.7 + - - +
42C SER* 3.6 7.5 + - - +
43C GLN* 3.1 33.3 + - - +
16E C 4.4 4.9 - - - +
17E T 3.1 31.2 - - + +
18E G 3.7 6.1 - - - +
19E C 6.0 0.2 - - - +
14F G 4.8 3.8 - - - +
15F C 3.7 27.4 - - + +
16F A 4.2 4.5 - - - +
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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
----------------------------------------------------------
11C TYR* 4.2 0.2 - - - -
36C GLN* 3.7 21.1 - - - +
37C SER* 2.7 20.9 + - - -
39C PRO* 1.3 75.9 - - - +
41C VAL* 1.3 57.6 + - - +
43C GLN* 3.2 7.3 + - - +
44C THR* 2.9 36.4 + - - +
14E G 5.4 0.7 - - + -
15E G 4.0 26.4 - - + +
16E C 2.7 45.2 + - - +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.2 25.8 - - + +
27C ARG* 3.5 37.2 - - + +
30C ILE* 4.4 5.8 - - + +
31C ALA* 3.6 30.1 - - + +
36C GLN* 4.4 7.6 - - + +
37C SER 3.6 11.9 - - - +
38C GLY* 3.1 16.6 + - - +
40C THR* 1.3 73.1 - - - +
42C SER* 1.3 71.3 + - - +
44C THR* 3.1 1.0 + - - -
45C VAL* 2.8 29.0 + - - +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 3.8 22.6 + - - +
38C GLY 3.2 8.3 + - - -
39C PRO* 3.8 11.2 - - - +
40C THR 3.4 0.2 - - - -
41C VAL* 1.3 82.7 - - - +
43C GLN* 1.3 61.4 + - - +
45C VAL* 3.7 2.3 - - - +
46C SER* 2.8 33.9 + - - -
13F G 4.9 2.6 - - - -
14F G 2.7 28.2 + - - -
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Residues in contact with GLN 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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43A GLN* 5.4 6.8 - - - +
39C PRO* 3.1 20.0 + - - +
40C THR* 3.7 4.0 - - - +
42C SER* 1.3 79.0 - - - +
44C THR* 1.3 65.6 + - - +
46C SER* 3.4 7.9 + - - -
47C ARG* 3.2 37.6 + - - +
14E G 5.8 1.0 - - - +
15E G 4.0 12.3 - - - +
16E C 3.2 19.2 + - - +
15F C 6.0 2.8 - - - -
16F A 4.6 9.9 + - - +
17F G 3.4 21.2 + - - -
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR* 3.7 22.8 - - + +
8C THR* 5.4 1.8 - - - +
11C TYR* 3.4 38.6 + - + -
40C THR* 2.9 22.5 + - - +
43C GLN* 1.3 76.5 - - - +
45C VAL* 1.3 59.4 + - - +
47C ARG* 3.4 31.3 + - - +
48C MET* 3.1 29.5 + - + +
14E G 4.4 7.8 - - - +
15E G 5.0 0.3 + - - -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.8 22.7 - - + -
27C ARG* 3.9 23.1 - - + +
30C ILE* 4.8 1.3 - - + -
41C VAL 2.8 19.9 + - - +
42C SER 3.7 3.4 - - - +
44C THR* 1.3 74.7 - - - +
46C SER* 1.3 55.0 + - - +
48C MET* 3.0 7.5 + - - +
49C GLU* 2.7 34.1 + - - +
54C LEU* 3.8 17.7 - - + +
56C VAL* 3.8 29.8 - - + -
62C LEU* 4.2 16.2 - - + -
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Residues in contact with SER 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 SER* 2.8 22.3 + - - -
43C GLN* 3.5 9.4 - - - -
45C VAL* 1.3 75.3 - - - +
47C ARG* 1.3 53.5 + - - +
49C GLU* 3.1 15.4 + - - +
50C ARG* 2.7 36.4 + - - +
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Residues in contact with ARG 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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7C THR* 5.1 0.4 - - - +
43C GLN* 3.2 29.1 + - - +
44C THR* 3.4 34.8 + - - +
45C VAL 3.1 0.6 - - - -
46C SER* 1.3 78.1 - - - +
48C MET* 1.3 57.9 + - + +
50C ARG* 3.1 27.2 + - - +
51C ASP* 2.8 36.3 + - - +
13E A 3.6 45.2 + - - +
14E G 2.9 53.3 + - - +
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Residues in contact with MET 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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8C THR* 3.7 31.0 - - + +
11C TYR* 3.6 33.7 - - + -
12C LEU* 3.5 39.5 - - + +
44C THR* 3.1 21.1 - - + +
45C VAL* 3.0 8.4 + - - +
47C ARG* 1.3 76.9 - - + +
49C GLU* 1.3 59.3 + - - +
51C ASP* 3.3 10.0 + - - -
53C LEU* 2.8 38.6 + - + +
54C LEU* 4.1 23.1 - - + -
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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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45C VAL 2.7 10.0 + - - +
46C SER* 3.1 19.9 + - - +
48C MET* 1.3 72.3 - - - +
50C ARG* 1.3 67.0 + - - +
51C ASP 2.9 1.1 - - - -
52C GLY* 2.8 17.0 + - - -
54C LEU* 3.4 23.1 - - + +
55C ARG* 4.2 5.0 - - + +
56C VAL* 3.4 45.0 + - - +
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Residues in contact with ARG 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 SER 2.7 17.0 + - - +
47C ARG* 3.3 28.2 + - - +
49C GLU* 1.3 71.8 - - - +
51C ASP* 1.3 94.0 + - - +
52C GLY 3.3 2.1 + - - -
12E C 4.8 1.0 + - - -
13E A 2.8 43.2 + - - -
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Residues in contact with ASP 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 ARG* 2.8 18.2 + - - +
48C MET* 3.9 5.7 - - - +
49C GLU 2.9 0.8 + - - -
50C ARG* 1.3 119.9 + - - +
52C GLY* 1.3 64.3 + - - +
53C LEU* 2.9 18.6 + - + +
67C LYS* 3.6 16.6 + - - +
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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