Contacts of the helix formed by residues 21 - 35 (chain G) in PDB entry 5IY8
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 ASN 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G GLY* 3.2 1.5 - - - -
20G PRO* 1.3 85.2 - - + +
22G LEU* 1.3 55.6 + - - +
23G LEU 3.5 1.8 - - - -
24G ASN* 3.2 41.3 + - - +
25G THR* 2.3 36.3 + - - +
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Residues in contact with LEU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475A LEU* 4.2 14.6 - - + -
1477A ALA* 3.8 30.7 - - + +
1480A CYS* 5.4 4.0 - - - -
13G LEU* 3.7 24.2 - - + -
17G TYR 3.3 24.5 - - - +
18G PHE* 3.9 11.2 - - + -
19G GLY 3.3 19.9 + - - +
20G PRO 3.3 4.2 + - - -
21G ASN* 1.3 74.3 - - - +
23G LEU* 1.3 61.8 + - - +
25G THR* 3.1 7.9 + - - -
26G VAL* 2.8 35.2 + - + +
68G TYR* 3.4 24.0 - - - +
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Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477A ALA* 5.0 9.2 - - + +
21G ASN 3.5 0.4 - - - -
22G LEU* 1.3 80.9 - - - +
24G ASN* 1.3 57.6 + - - +
26G VAL* 3.5 7.9 + - + +
27G LYS* 3.1 40.8 + - + +
54G ILE* 3.6 33.9 - - + -
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Residues in contact with ASN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASN* 3.2 37.2 + - - +
22G LEU 3.4 0.8 - - - -
23G LEU* 1.3 75.5 - - - +
25G THR* 1.3 55.5 + - - +
27G LYS* 3.1 18.6 + - + +
28G GLN* 2.8 57.0 + - - +
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Residues in contact with THR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU* 5.2 5.6 - - + -
17G TYR* 4.0 34.6 + - + +
21G ASN* 2.3 33.2 + - - +
22G LEU* 3.2 11.6 - - - -
24G ASN* 1.3 74.6 - - - +
26G VAL* 1.3 60.1 + - - +
28G GLN* 3.2 10.9 + - + +
29G LYS* 2.8 29.6 + - + +
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.5 20.2 - - + +
13G LEU* 3.6 29.8 - - + -
22G LEU* 2.8 27.0 + - + +
23G LEU* 3.6 11.0 - - + +
25G THR* 1.3 72.2 - - - +
27G LYS* 1.3 59.9 + - - +
29G LYS* 3.1 9.3 + - - +
30G LEU* 2.9 28.9 + - + +
54G ILE* 5.1 15.9 - - + -
68G TYR* 4.1 25.6 - - + -
70G VAL* 5.2 6.1 - - + -
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Residues in contact with LYS 27 (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 LEU* 3.1 30.3 + - + +
24G ASN* 3.1 20.9 + - + +
26G VAL* 1.3 79.4 - - - +
28G GLN* 1.3 61.3 + - + +
30G LEU* 3.4 7.1 + - - +
31G PHE* 2.9 37.2 + - + -
51G ILE* 3.6 29.6 - - + -
54G ILE* 4.4 13.2 - - + -
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Residues in contact with GLN 28 (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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54D GLU* 5.0 16.1 + - - +
24G ASN* 2.8 44.9 + - - +
25G THR* 3.6 8.3 - - - +
27G LYS* 1.3 72.0 - - - +
29G LYS* 1.3 59.6 + - - +
31G PHE* 3.3 9.6 + - + +
32G THR* 2.8 33.8 + - - +
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Residues in contact with LYS 29 (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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11G ILE* 5.0 10.9 - - + +
12G LEU* 2.8 28.8 + - - +
13G LEU* 3.6 31.3 - - + +
14G HIS* 5.0 2.6 - - - +
17G TYR* 4.4 19.3 - - + -
25G THR* 2.8 16.1 + - + +
26G VAL* 3.1 10.1 + - - +
28G GLN* 1.3 75.8 - - - +
30G LEU* 1.3 57.1 + - - +
32G THR* 3.3 8.9 + - - -
33G GLU* 3.0 37.0 + - + +
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Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G HIS* 4.5 7.6 - - + -
11G ILE* 3.7 31.5 - - + +
26G VAL* 2.9 13.4 + - + +
27G LYS* 3.4 10.1 - - - +
29G LYS* 1.3 74.0 - - - +
31G PHE* 1.3 68.0 + - + +
33G GLU 3.1 1.7 + - - -
34G VAL* 3.0 59.3 + - + +
48G VAL* 5.1 6.7 - - + -
51G ILE* 4.2 24.0 - - + -
70G VAL* 4.0 30.1 - - + -
72G TYR* 4.9 14.1 - - + -
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Residues in contact with PHE 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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44D ARG* 3.9 22.2 - - - +
47D GLN* 6.1 0.4 - - - -
54D GLU* 5.3 4.9 - - - -
27G LYS* 2.9 30.7 + - + +
28G GLN* 3.4 13.0 - - + +
30G LEU* 1.3 83.3 - - + +
32G THR* 1.3 61.9 + - - +
34G VAL* 4.8 0.9 - - - -
35G GLU* 3.0 61.8 + - + +
48G VAL* 4.6 27.6 - - + -
49G THR 6.5 0.2 - - - -
51G ILE* 4.4 19.5 - - + -
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Residues in contact with THR 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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55D GLN* 4.2 28.8 + - - +
28G GLN* 2.8 19.2 + - - +
29G LYS* 3.7 9.2 - - - -
30G LEU 3.2 0.4 - - - -
31G PHE* 1.3 77.2 - - - +
33G GLU* 1.3 60.2 + - - +
35G GLU 4.6 5.7 - - - +
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Residues in contact with GLU 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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9G HIS* 2.8 32.4 + - - -
10G GLU 4.4 1.2 - - - +
11G ILE* 3.1 23.8 - - - +
12G LEU 5.2 1.6 + - - -
29G LYS* 3.0 23.6 + - + +
30G LEU* 3.1 2.9 + - - +
32G THR* 1.3 78.3 - - - +
34G VAL* 1.3 61.1 + - + +
37G THR* 3.2 19.6 - - - +
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G HIS* 4.2 18.8 - - + +
30G LEU* 3.0 41.6 + - + +
33G GLU* 1.3 84.7 - - + +
35G GLU* 1.3 72.2 + - + +
36G GLY 3.4 0.5 + - - -
37G THR* 2.5 28.9 + - - +
45G VAL* 4.0 17.1 - - + +
48G VAL* 3.7 29.6 - - + -
72G TYR* 5.1 11.7 - - + +
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ARG* 3.3 29.6 + - - -
57D LEU* 4.9 6.4 - - - +
31G PHE* 3.0 59.6 + - - +
32G THR 4.6 6.8 - - - +
34G VAL* 1.3 83.2 - - + +
36G GLY* 1.3 59.0 + - - +
37G THR* 3.2 6.6 + - - +
45G VAL* 4.6 5.2 - - + -
46G ILE 5.2 4.0 - - - +
47G ALA* 5.0 5.2 - - - -
48G VAL* 4.3 19.9 + - + +
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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