Contacts of the helix formed by residues 51 - 64 (chain G) in PDB entry 4UN7
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 HIS 51 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13G TYR* 2.6 36.0 + + - -
17G LEU* 5.4 0.2 - - + -
46G ASN 3.9 0.4 + - - +
47G LEU* 3.1 38.9 + - + +
50G GLN* 1.3 82.0 - - + +
52G ILE* 1.3 73.9 + - + +
54G PRO* 3.7 6.0 - - - +
55G LEU* 3.5 34.6 - - + +
115G VAL* 5.8 1.6 - - + -
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Residues in contact with ILE 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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13G TYR* 5.7 0.2 - - + -
14G LEU* 4.4 6.5 - - + +
17G LEU* 3.6 35.2 - - + -
40G ILE* 4.2 25.1 - - + -
42G GLN* 4.8 5.8 - - - +
47G LEU* 3.0 33.7 + - + +
48G ILE* 3.6 23.6 - - + +
51G HIS* 1.3 84.3 - - + +
53G ALA* 1.3 67.3 + - - +
54G PRO 3.3 1.6 - - - -
55G LEU* 3.0 18.6 + - - +
56G MET* 3.0 11.9 + - + +
80G LEU* 4.2 15.0 - - + -
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Residues in contact with ALA 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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48G ILE 2.7 21.8 + - - +
49G LYS* 3.9 10.3 - - - +
52G ILE* 1.3 72.3 - - - +
54G PRO* 1.3 69.5 - - + +
56G MET* 3.2 2.7 + - - +
57G GLN* 2.8 25.8 + - - +
69G ILE* 3.8 11.1 - - + +
71G ILE* 4.6 10.3 - - + -
80G LEU* 3.6 20.6 - - + +
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Residues in contact with PRO 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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49G LYS 3.3 21.1 - - - +
50G GLN* 3.3 19.3 - - - +
51G HIS 3.7 12.6 - - - +
52G ILE 3.4 3.8 - - - -
53G ALA* 1.3 89.7 - - + +
55G LEU* 1.3 56.3 + - + +
57G GLN* 3.4 8.2 - - + +
58G PHE* 3.2 24.1 + - - +
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Residues in contact with LEU 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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10G ILE* 4.1 42.3 - - + +
13G TYR* 3.9 32.1 - - + -
14G LEU* 4.3 9.0 - - + -
51G HIS* 3.5 30.3 - - + +
52G ILE* 3.0 9.7 + - - +
54G PRO* 1.3 78.1 - - + +
56G MET* 1.3 64.9 + - - +
58G PHE* 3.3 9.0 + - + +
59G LEU* 3.2 20.6 + - - +
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Residues in contact with MET 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 4.1 21.2 - - + +
18G ILE* 4.8 0.9 - - + -
38G VAL* 3.9 26.0 - - + -
40G ILE* 4.4 16.6 - - + -
52G ILE* 3.0 15.4 + - + +
53G ALA* 3.8 7.2 - - - +
55G LEU* 1.3 74.2 - - - +
57G GLN* 1.3 60.2 - - - +
59G LEU* 3.4 6.5 + - - +
60G ILE* 3.0 35.3 + - + +
69G ILE* 3.9 14.6 - - + -
80G LEU* 4.2 21.8 - - + -
82G VAL* 4.0 13.9 - - + -
87G LEU* 3.8 20.4 - - + -
91G PHE* 4.3 12.3 - - + -
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Residues in contact with GLN 57 (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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53G ALA 2.8 16.9 + - - +
54G PRO* 3.4 10.5 - - + +
56G MET* 1.3 74.9 - - - +
58G PHE* 1.3 65.7 + - - +
60G ILE* 3.2 15.0 + - - +
61G ASP* 2.9 54.7 + - - +
69G ILE* 3.4 25.0 + - + +
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Residues in contact with PHE 58 (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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6G GLU* 4.0 20.4 - - - -
7G VAL* 3.8 34.3 - - + -
10G ILE* 3.7 34.8 - - + -
54G PRO 3.2 11.0 + - - +
55G LEU* 3.4 12.6 - - + +
56G MET 3.3 0.4 - - - -
57G GLN* 1.3 79.0 - - - +
59G LEU* 1.3 61.5 + - + +
61G ASP* 3.2 11.1 + - + +
62G GLU* 2.9 47.5 + - + +
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Residues in contact with LEU 59 (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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7G VAL* 4.2 15.5 - - + +
10G ILE* 5.2 2.7 - - + -
11G SER* 3.6 26.2 - - - +
14G LEU* 3.8 14.8 - - + -
55G LEU 3.2 10.2 + - - +
56G MET* 3.7 11.0 - - - +
58G PHE* 1.3 87.1 - - + +
60G ILE* 1.3 57.3 + - - +
62G GLU* 3.2 3.2 + - + +
63G LEU* 3.0 52.1 + - + +
87G LEU* 4.2 6.1 - - + -
90G TYR* 4.1 9.6 - - + +
91G PHE* 3.3 36.3 - - + -
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Residues in contact with ILE 60 (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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56G MET* 3.0 19.1 + - + +
57G GLN* 3.6 16.2 - - - +
58G PHE 3.2 0.2 - - - -
59G LEU* 1.3 73.9 - - - +
61G ASP* 1.3 65.6 + - - +
63G LEU 3.5 0.5 + - - -
64G ASN* 3.0 4.5 + - - -
65G VAL* 3.0 68.6 + - + +
67G SER 4.2 10.3 - - - +
69G ILE* 3.5 32.5 - - + -
82G VAL* 3.9 27.4 - - + -
87G LEU* 4.4 13.2 - - + -
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Residues in contact with ASP 61 (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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57G GLN* 2.9 45.2 + - - +
58G PHE* 3.5 11.4 - - + +
60G ILE* 1.3 77.4 - - - +
62G GLU* 1.3 63.8 + - - +
64G ASN* 3.5 16.4 + - - +
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Residues in contact with GLU 62 (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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7G VAL* 3.5 35.3 - - + +
58G PHE* 2.9 36.5 + - + +
59G LEU* 3.7 7.2 - - - +
60G ILE 3.2 0.2 - - - -
61G ASP* 1.3 81.5 - - - +
63G LEU* 1.3 61.3 + - + +
64G ASN* 4.5 5.5 + - - -
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Residues in contact with LEU 63 (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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7G VAL* 5.2 6.7 - - + -
59G LEU* 3.0 33.6 + - + +
62G GLU* 1.3 80.3 - - + +
64G ASN* 1.3 60.8 + - - +
65G VAL* 4.3 11.2 - - + -
86G LYS* 2.5 43.7 + - + +
87G LEU* 3.7 31.2 - - + -
90G TYR* 3.7 40.6 - - + +
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Residues in contact with ASN 64 (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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60G ILE 3.0 7.4 + - - -
61G ASP* 3.5 9.6 + - - +
62G GLU 3.4 8.3 + - - -
63G LEU* 1.3 81.5 - - - +
65G VAL* 1.3 62.8 + - - +
66G LYS* 3.6 4.0 + - - +
86G LYS* 4.0 10.9 + - - +
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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