Contacts of the helix formed by residues 40 - 55 (chain H) in PDB entry 7C17
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 THR 40 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H THR* 4.3 0.8 - - - +
39H TYR* 1.3 73.7 - - - +
41H GLN* 1.3 62.5 + - - +
42H GLN* 3.7 10.3 + - + +
43H HIS* 3.4 35.2 + - + +
44H LEU* 2.7 34.7 + - - +
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H THR* 1.3 80.7 + - - +
42H GLN* 1.3 59.1 + - - +
44H LEU* 3.3 25.4 + - - +
45H ASN* 2.9 43.5 + - - +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H THR* 3.4 10.3 + - + +
41H GLN* 1.3 75.2 - - - +
43H HIS* 1.3 61.3 + - + +
45H ASN* 3.2 12.2 + - - +
46H GLU* 2.9 44.6 + - - +
70H PHE* 3.8 37.9 + - - -
71H ASN* 5.8 1.4 - - - +
73H PRO* 5.5 6.7 - - - +
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Residues in contact with HIS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H VAL* 6.4 0.2 - - + -
27H THR* 3.6 24.2 + - + +
28H PRO 4.5 2.0 + - - -
29H PRO* 4.1 23.0 - - + +
30H MET* 4.9 2.5 - - + -
38H THR 4.2 3.5 + - - -
39H TYR* 3.6 31.1 - + + -
40H THR* 3.3 38.4 + - + +
42H GLN* 1.3 79.3 - - + +
44H LEU* 1.3 57.8 + - - +
46H GLU* 3.2 24.7 + - - +
47H LEU* 2.9 29.9 + - - +
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 3.9 29.8 - - + +
9H ILE* 4.1 27.6 - - + -
10H THR* 5.5 0.7 - - - -
39H TYR* 4.8 3.8 - - + +
40H THR 2.7 20.9 + - - +
41H GLN* 3.6 32.1 - - - +
42H GLN 3.3 0.2 - - - -
43H HIS* 1.3 70.6 - - - +
45H ASN* 1.3 62.5 + - - +
47H LEU* 3.4 7.5 + - + +
48H THR* 2.8 39.4 + - + +
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Residues in contact with ASN 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G SER* 4.3 14.4 + - - +
41H GLN* 2.9 28.6 + - - +
42H GLN* 3.2 19.2 + - - +
44H LEU* 1.3 77.9 - - - +
46H GLU* 1.3 59.3 + - - +
48H THR* 3.0 8.6 + - - -
49H LEU* 2.9 30.1 + - - +
70H PHE* 4.0 20.8 - - + -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H VAL* 5.9 0.9 - - - +
27H THR* 3.4 16.3 - - - +
42H GLN* 2.9 31.4 + - + +
43H HIS* 3.2 31.2 - - - +
44H LEU 3.3 0.2 - - - -
45H ASN* 1.3 75.4 - - - +
47H LEU* 1.3 58.4 + - - +
49H LEU* 3.3 3.2 + - - +
50H LEU* 2.9 36.0 + - + +
67H VAL* 3.9 18.7 - - + +
70H PHE* 3.6 27.1 - - + -
71H ASN* 3.7 26.6 - - + +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H ILE* 3.7 28.7 - - + -
6H VAL* 3.8 18.8 - - + -
10H THR* 3.4 26.4 + - + +
12H LEU* 5.3 0.9 - - + -
17H ILE* 3.9 28.5 - - + -
39H TYR* 5.1 9.9 - - + -
43H HIS 2.9 17.4 + - - +
44H LEU* 3.7 7.4 - - + +
45H ASN 3.3 0.2 - - - -
46H GLU* 1.3 77.7 - - - +
48H THR* 1.3 57.8 + - - +
50H LEU* 3.4 29.2 - - + +
51H ARG* 2.9 30.7 + - - +
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Residues in contact with THR 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G SER* 3.9 15.8 - - - -
9H ILE* 4.6 13.2 - - + +
10H THR* 4.4 13.5 - - - +
44H LEU* 2.8 37.5 + - + +
45H ASN* 3.0 17.5 + - - -
47H LEU* 1.3 72.7 - - - +
49H LEU* 1.3 58.0 + - - +
51H ARG* 4.5 2.2 - - - +
52H GLN* 2.9 39.7 + - - +
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 3.8 38.8 - - + -
126G LEU* 4.9 14.4 - - + -
127G SER* 4.1 13.9 - - - +
45H ASN 2.9 19.0 + - - +
46H GLU 3.6 4.0 - - - +
48H THR* 1.3 77.0 + - - +
50H LEU* 1.3 62.2 + - - +
52H GLN* 3.4 11.8 + - + -
53H ALA* 3.4 14.9 + - + +
63H SER* 4.2 0.6 + - - +
66H LEU* 4.3 21.8 - - + +
67H VAL* 4.5 9.0 - - + -
70H PHE* 3.7 39.3 - - + -
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Residues in contact with LEU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H LEU* 4.7 1.6 - - + -
17H ILE* 6.2 0.4 - - + -
20H TYR* 3.6 36.3 - - + -
25H LEU* 5.3 3.8 - - + -
26H VAL* 4.4 22.9 - - + -
46H GLU* 2.9 24.5 + - + +
47H LEU* 3.4 28.9 - - + +
49H LEU* 1.3 78.7 - - - +
51H ARG* 1.3 63.2 + - + +
54H ARG* 3.1 31.9 + - - +
63H SER* 3.5 17.9 + - - +
67H VAL* 4.2 23.1 - - + -
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H THR* 3.2 39.5 - - - +
12H LEU* 4.4 17.7 - - + -
47H LEU 2.9 10.3 + - - +
48H THR* 4.3 2.7 - - - +
50H LEU* 1.3 74.7 - - - +
52H GLN* 1.3 62.4 + - - +
53H ALA 3.2 6.1 + - - -
54H ARG* 4.2 2.5 - - - +
55H GLN* 3.6 28.1 + - + +
56H VAL* 4.1 4.3 - - - +
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Residues in contact with GLN 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LEU* 3.4 40.5 + - + +
127G SER* 5.7 0.2 - - - -
48H THR* 2.9 29.0 + - - +
49H LEU* 3.8 7.6 - - + +
50H LEU 3.4 0.8 - - - -
51H ARG* 1.3 76.7 - - - +
53H ALA* 1.3 56.8 + - - +
56H VAL* 3.3 34.1 - - + +
57H GLY* 3.7 3.6 + - - -
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H LEU* 3.4 9.8 + - + +
51H ARG 3.2 0.2 - - - -
52H GLN* 1.3 79.4 - - - +
54H ARG* 1.3 62.0 + - - +
55H GLN 3.4 0.7 - - - -
57H GLY* 2.6 15.8 + - - +
58H PHE* 2.3 55.0 + - + +
63H SER* 3.4 21.8 - - - +
66H LEU* 4.8 6.5 - - + -
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Residues in contact with ARG 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382 A 3.4 38.2 + - - -
392 G 3.2 34.3 + - - +
12H LEU* 6.4 1.1 - - + -
20H TYR* 3.4 14.4 - - + +
50H LEU 3.1 18.8 + - - +
51H ARG* 5.0 1.6 - - - -
53H ALA* 1.3 77.7 - - - +
55H GLN* 1.3 65.5 + - + +
58H PHE 3.0 22.1 + - - +
59H ASN* 3.5 12.6 - - - +
60H LEU* 3.4 26.8 - - - +
63H SER* 4.2 5.4 + - - +
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Residues in contact with GLN 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392 G 4.0 15.8 + - - +
11H GLY 5.2 4.6 + - - +
12H LEU* 4.1 30.2 - - + +
51H ARG* 3.6 17.8 + - + +
54H ARG* 1.3 85.1 - - + +
56H VAL* 1.3 64.6 + - + +
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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