Contacts of the helix formed by residues 42 - 56 (chain G) in PDB entry 4U7B
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 42 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29G HIS* 3.6 5.4 - - - -
40G VAL 5.6 0.4 - - - +
41G PRO* 1.3 78.8 - - - +
43G VAL* 1.3 63.4 + - - +
44G LYS* 3.2 19.4 + - - +
45G THR* 2.7 28.6 + - - +
46G CYS* 3.4 12.6 + - - -
22H G 3.2 35.1 + - + +
23H T 3.7 23.8 - - + +
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Residues in contact with VAL 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ALA 4.4 0.9 - - - -
26G ALA* 3.5 38.4 - - + +
29G HIS* 3.5 34.0 + - + +
42G THR* 1.3 74.3 - - - +
44G LYS* 1.3 65.8 + - + +
46G CYS* 3.1 3.2 + - - +
47G GLU* 2.8 46.1 + - - +
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Residues in contact with LYS 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G THR* 3.2 7.2 + - - +
43G VAL* 1.3 84.2 - - + +
45G THR* 1.3 57.3 + - - +
47G GLU* 3.2 23.5 + - + +
48G ARG* 2.9 68.8 + - - +
23H T 3.4 33.9 - - + -
24H C 4.6 4.3 - - - +
32I C 3.9 13.8 - - + +
33I G 2.7 46.4 + - - +
34I A 3.8 1.8 - - - +
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Residues in contact with THR 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 5.0 0.7 - - - -
41G PRO* 3.5 10.2 - - + +
42G THR* 2.7 32.0 + - - +
44G LYS* 1.3 75.3 - - - +
46G CYS* 1.3 58.1 + - - -
48G ARG* 3.1 18.4 + - - +
49G TRP* 2.9 38.2 + - - +
21H T 3.3 58.3 - - + +
22H G 3.3 1.9 + - - +
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Residues in contact with CYS 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 3.8 25.3 - - + +
25G ALA* 4.2 18.4 - - + +
28G SER* 5.1 0.4 - - - -
29G HIS* 3.9 22.4 - - - +
32G LEU* 3.9 24.7 - - - -
41G PRO* 4.9 4.9 - - - -
42G THR 3.5 13.9 - - - -
43G VAL* 3.1 10.2 + - - +
45G THR* 1.3 78.6 + - - +
47G GLU* 1.3 61.3 + - - +
49G TRP* 4.1 0.3 - - - +
50G PHE* 3.1 33.8 + - + -
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ALA* 3.6 24.0 - - + -
43G VAL* 2.8 37.4 + - + +
44G LYS* 3.3 20.9 + - + +
45G THR 3.1 0.2 - - - -
46G CYS* 1.3 77.2 - - - +
48G ARG* 1.3 57.7 + - - +
50G PHE* 3.4 5.2 - - - +
51G GLN* 3.1 20.6 + - - +
30I A 5.4 0.9 - - - +
31I A 3.9 29.2 + - + +
32I C 3.2 53.5 + - - +
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 2.9 53.3 + - + +
45G THR* 3.5 21.8 - - - +
47G GLU* 1.3 74.3 - - - +
49G TRP* 1.3 67.6 + - + +
50G PHE 3.3 0.4 - - - -
51G GLN* 3.2 32.5 + - - +
52G ARG* 3.3 8.8 + - - +
20H A 5.9 0.7 - - - -
21H T 3.5 36.4 + - - +
22H G 2.9 49.3 + - - -
34I A 3.9 3.8 - - - +
35I C 4.3 2.6 - - - +
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Residues in contact with TRP 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG* 3.6 55.1 - - + +
15G LEU* 4.0 22.4 - - + -
45G THR* 2.9 28.3 + - + +
48G ARG* 1.3 78.7 - - + +
50G PHE* 1.3 63.8 + - - +
52G ARG* 3.4 44.3 + - - +
53G PHE* 3.3 57.1 + + + -
59G ASP 3.4 23.3 - - - -
60G VAL 4.1 3.8 - - - -
61G ASP 4.5 3.1 - - - -
62G ASP* 5.6 0.2 - - - -
20H A 4.4 10.1 - - - +
21H T 2.6 29.2 + - - -
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Residues in contact with PHE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 3.6 34.5 - - + -
18G CYS 4.4 0.2 - - - -
19G PHE* 3.7 39.8 - + + -
23G LYS 3.4 21.1 - - - -
24G THR 4.1 1.3 - - - -
25G ALA* 3.9 20.2 - - + -
28G SER* 3.5 25.8 - - - -
46G CYS* 3.1 27.3 + - + +
47G GLU* 3.4 8.1 - - - +
48G ARG 3.3 0.2 - - - -
49G TRP* 1.3 77.0 - - - +
51G GLN* 1.3 66.5 + - - +
53G PHE* 2.9 23.7 + + - +
54G LYS* 3.2 26.7 + - - +
31I A 5.8 0.2 - - - -
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G GLU 3.1 10.0 + - - +
48G ARG* 3.2 23.0 + - - +
50G PHE* 1.3 78.1 - - - +
52G ARG* 1.3 60.0 + - - +
54G LYS* 3.5 18.1 + - + +
55G SER* 3.5 15.8 + - - -
32I C 4.4 26.8 + - - +
33I G 5.4 6.0 + - - -
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Residues in contact with ARG 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ARG 3.3 8.2 + - - +
49G TRP* 3.4 56.5 - - + +
50G PHE 3.0 1.0 - - - -
51G GLN* 1.3 76.2 - - - +
53G PHE* 1.3 67.9 + - + +
54G LYS 3.1 2.0 - - - -
55G SER* 3.1 20.9 + - - -
56G GLY 3.3 7.4 + - - -
57G ASP* 3.3 40.4 + - - +
59G ASP 3.6 10.5 + - - -
61G ASP 4.1 6.5 + - - -
63G LYS* 4.1 24.2 - - - +
20H A 3.2 34.4 + - - -
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Residues in contact with PHE 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG 4.3 4.7 - - - -
15G LEU* 3.3 35.7 - - + -
16G ILE* 3.2 37.0 - - + -
19G PHE* 3.9 34.4 - + + -
49G TRP* 3.3 48.4 + + - -
50G PHE* 2.9 13.6 + + - +
52G ARG* 1.3 78.8 - - + +
54G LYS* 1.3 60.9 + - - +
56G GLY* 3.2 10.0 + - - -
57G ASP 3.7 17.9 - - - -
58G PHE* 3.3 26.5 - + + -
59G ASP 5.2 0.7 - - - -
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Residues in contact with LYS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G PHE* 3.9 24.7 - - + -
50G PHE* 3.2 26.1 + - - +
51G GLN* 3.6 16.5 - - + +
52G ARG 3.1 0.4 - - - -
53G PHE* 1.3 76.0 - - - +
55G SER* 1.3 63.4 + - - +
56G GLY* 3.4 0.9 + - - -
31I A 5.3 5.7 + - - -
32I C 4.6 13.1 + - - -
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Residues in contact with SER 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G GLN 3.5 6.8 + - - -
52G ARG* 3.1 17.6 + - - -
54G LYS* 1.3 78.3 - - - +
56G GLY* 1.3 57.3 + - - +
57G ASP* 3.8 7.7 + - - -
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Residues in contact with GLY 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ARG 3.3 0.4 + - - -
53G PHE 3.2 12.2 + - - -
54G LYS 4.3 0.9 - - - -
55G SER* 1.3 81.1 - - - +
57G ASP* 1.3 60.7 + - - +
58G PHE* 3.1 21.9 + - - -
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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