Contacts of the strand formed by residues 30 - 39 (chain G) in PDB entry 5IXM
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 PHE 30 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G ASN* 4.2 1.4 - - - +
26G ILE* 3.4 28.0 + - + +
27G ALA* 2.6 45.5 + - + +
28G PRO 3.5 0.2 - - - -
29G ASN* 1.3 116.6 - - - +
31G ASP* 1.3 61.2 + - - +
50G PHE* 3.3 29.6 - + + -
51G ARG 3.7 3.4 - - - -
52G TYR* 4.4 5.6 - + + -
54G LEU* 3.8 25.6 - - + -
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Residues in contact with ASP 31 (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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23G TYR* 2.9 36.6 - - - +
24G TRP 4.1 3.8 - - - -
25G ASN* 5.2 2.7 - - - +
26G ILE* 3.9 2.4 - - - +
27G ALA 5.4 0.2 - - - +
30G PHE* 1.3 75.6 - - - +
32G ALA* 1.3 70.0 + - - +
33G THR* 4.6 3.9 + - - -
49G GLU* 4.8 1.2 - - - +
50G PHE* 2.9 23.5 - - - -
51G ARG* 2.8 74.6 + - + +
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Residues in contact with ALA 32 (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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23G TYR* 3.4 5.9 - - - -
24G TRP* 2.8 62.8 + - + +
26G ILE* 4.8 3.8 - - + +
31G ASP* 1.3 78.4 - - - +
33G THR* 1.3 67.5 + - - +
34G ILE* 4.6 4.0 - - + -
49G GLU 3.3 8.7 - - - +
50G PHE* 4.5 9.6 - - + -
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Residues in contact with THR 33 (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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4G LEU* 6.0 3.8 - - + +
21G PRO* 4.8 7.6 - - + -
22G TYR 3.6 10.5 - - - +
23G TYR* 4.2 14.0 - - + +
31G ASP* 4.6 4.7 + - - -
32G ALA* 1.3 78.6 + - - +
34G ILE* 1.3 64.6 + - - +
35G THR* 3.7 17.9 - - - +
47G GLN 3.4 4.3 - - - +
48G ASN* 3.5 1.7 - - - -
49G GLU* 2.8 49.6 + - + +
51G ARG* 5.6 0.9 + - - -
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Residues in contact with ILE 34 (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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21G PRO* 3.5 0.3 - - - +
22G TYR* 2.8 58.5 + - + +
24G TRP* 3.8 41.5 - - + -
32G ALA* 4.6 2.5 - - + -
33G THR* 1.3 80.1 - - - +
35G THR* 1.3 65.0 + - - +
36G PRO* 3.9 5.2 - - + +
46G TRP* 4.5 22.0 - - + -
47G GLN 3.5 3.4 - - - +
48G ASN* 4.0 20.4 - - + +
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Residues in contact with THR 35 (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 LEU* 3.9 19.7 - - + -
20G LEU 3.8 18.2 - - - +
21G PRO* 3.4 20.9 - - + +
33G THR* 3.7 12.3 - - - +
34G ILE* 1.3 81.7 + - - +
36G PRO* 1.3 74.2 - - - +
37G HIS 3.5 2.1 + - - -
46G TRP* 3.7 1.5 - - - -
47G GLN* 2.9 52.7 + - - +
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Residues in contact with PRO 36 (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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18G PHE* 3.7 2.1 - - - +
20G LEU* 2.9 62.7 + - + +
22G TYR* 6.1 0.4 - - + -
34G ILE* 3.9 5.8 - - + +
35G THR* 1.3 86.3 - - - +
37G HIS* 1.3 58.2 + - - +
38G TYR 4.1 1.6 - - - -
44G LEU* 4.2 13.7 - - + -
45G GLN 3.4 7.4 - - - +
46G TRP* 3.8 36.3 - - + -
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Residues in contact with HIS 37 (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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9G LYS* 5.8 0.2 - - - -
17G GLU* 3.3 29.8 + - - +
18G PHE 3.3 6.5 - - - -
19G LEU* 3.4 40.1 - - + +
35G THR 4.3 4.3 - - - +
36G PRO* 1.3 72.7 - - - +
38G TYR* 1.3 67.9 + - - +
39G MET* 3.7 19.4 + - - +
43G GLY 3.9 0.5 - - - +
44G LEU* 3.9 1.3 - - - +
45G GLN* 2.8 62.8 + - + +
47G GLN* 3.8 12.4 + - + +
117G LEU* 5.9 0.2 - - + -
118G THR* 5.3 14.8 - - - -
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Residues in contact with TYR 38 (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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16G PHE* 4.4 11.4 - + + -
17G GLU* 3.2 5.7 - - - -
18G PHE* 2.9 51.5 + - + +
36G PRO 4.1 0.4 - - - -
37G HIS* 1.3 74.6 - - - +
39G MET* 1.3 71.1 + - - +
40G GLU* 3.5 40.8 + - + +
43G GLY* 3.8 14.4 - - - -
44G LEU* 3.9 18.2 - - + +
70G ARG* 4.8 6.7 + - - -
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Residues in contact with MET 39 (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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14G ASN* 3.8 23.1 - - + -
16G PHE 3.6 3.6 - - - -
17G GLU* 3.7 18.6 - - + +
37G HIS* 3.8 21.3 - - - +
38G TYR* 1.3 85.0 - - - +
40G GLU* 1.3 67.5 + - - +
41G ARG 3.3 0.9 - - - -
42G ARG* 3.1 13.2 + - + -
43G GLY* 2.9 42.1 + - - +
45G GLN* 3.7 30.5 - - + +
66G LEU* 4.1 11.4 - - + -
117G LEU* 3.6 33.9 - - + -
118G THR 6.0 0.7 - - - -
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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