Contacts of the helix formed by residues 30 - 41 (chain I) in PDB entry 6K4Y
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 ARG 30 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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903C ARG 5.2 1.2 + - - -
904C ALA 3.3 22.6 + - - -
905C ILE* 4.0 8.7 + - - +
906C PHE 5.2 2.0 + - - -
907C GLY* 5.3 6.3 - - - -
27I VAL 4.8 1.3 - - - -
28I GLU 3.7 7.9 + - - +
29I ASN* 1.3 82.7 + - - +
31I ALA* 1.3 58.6 + - - +
32I ASN 3.4 1.3 - - - -
33I PHE* 3.2 8.1 + - + +
34I ILE* 2.9 51.7 + - + +
51I GLN* 5.1 14.1 - - - +
54I PHE* 3.2 35.6 - - + -
55I ARG* 5.3 13.4 - - - +
47T A 4.7 22.7 + - - +
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Residues in contact with ALA 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598F LEU* 5.1 13.7 - - + +
29I ASN* 3.7 6.6 + - - +
30I ARG* 1.3 77.1 - - - +
32I ASN* 1.3 60.0 + - - +
34I ILE* 3.3 6.5 + - - +
35I ALA* 2.9 26.7 + - - +
51I GLN* 3.6 25.3 - - - +
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Residues in contact with ASN 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594F ALA* 5.2 2.4 - - - +
595F LEU* 3.7 35.3 - - + +
598F LEU* 5.1 3.8 - - + +
25I ASP 5.0 1.0 + - - -
26I ILE* 4.5 22.1 - - + +
29I ASN* 3.0 53.7 - - - +
31I ALA* 1.3 73.2 - - - +
33I PHE* 1.3 74.0 + - - +
35I ALA* 3.2 9.4 + - - +
36I PHE* 2.9 27.0 + - - +
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Residues in contact with PHE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C ILE* 3.7 31.4 - - + -
11I ILE* 4.9 6.3 - - + -
14I VAL* 5.9 1.3 - - + -
15I ALA* 4.7 13.7 - - + -
18I LEU* 4.9 13.0 - - + -
26I ILE* 2.9 24.0 - - + +
27I VAL* 3.7 25.4 - - + -
29I ASN 3.3 20.0 - - - +
30I ARG* 3.2 10.3 + - + +
32I ASN* 1.3 82.6 + - - +
34I ILE* 1.3 64.2 + - + +
36I PHE* 3.1 11.6 + + + +
37I LEU* 2.9 59.0 + - + +
54I PHE* 4.5 13.0 - + - -
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Residues in contact with ILE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG* 2.9 33.9 + - + +
31I ALA* 3.7 5.8 - - - +
33I PHE* 1.3 80.9 - - + +
35I ALA* 1.3 61.0 + - - +
37I LEU* 3.4 8.2 + - + +
38I ASN* 2.8 40.7 + - - +
49I LEU* 3.4 38.6 - - + +
50I ASN* 5.0 1.3 - - - -
51I GLN* 3.7 36.1 - - + +
54I PHE* 4.4 22.9 - - + -
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594F ALA* 4.0 20.6 - - - +
597F LYS* 5.8 2.9 - - + -
598F LEU* 4.0 17.9 - - + -
31I ALA 2.9 14.2 + - - +
32I ASN* 3.4 10.3 - - - +
33I PHE 3.2 0.2 - - - -
34I ILE* 1.3 77.9 - - - +
36I PHE* 1.3 56.2 + - - +
38I ASN* 3.8 7.3 - - - +
39I GLU* 2.9 35.9 + - + +
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Residues in contact with PHE 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563F PHE* 4.2 20.4 - + - -
587F ILE* 4.3 22.7 - - + -
590F ILE* 4.2 19.5 - - + -
591F GLU* 4.4 7.6 - - + -
594F ALA* 4.3 21.7 - - + +
14I VAL* 4.3 16.2 - - + -
18I LEU* 4.2 28.9 - - + -
26I ILE* 5.1 13.7 - - + -
32I ASN 2.9 13.2 + - - +
33I PHE* 3.3 15.3 - + + +
35I ALA* 1.3 76.6 - - - +
37I LEU* 1.3 71.0 + - + +
39I GLU* 3.3 2.5 + - - +
40I ILE* 3.0 44.8 + - + +
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Residues in contact with LEU 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 4.7 19.1 - - + -
14I VAL* 4.4 15.3 - - + -
33I PHE* 2.9 62.7 + - + +
34I ILE* 3.8 8.3 - - + +
36I PHE* 1.3 86.1 - - + +
38I ASN* 1.3 64.3 + - - +
40I ILE* 3.3 16.7 - - + +
41I GLY 3.2 14.9 + - - -
42I VAL* 3.3 46.1 + - + +
49I LEU* 5.5 5.4 - - + -
54I PHE* 6.0 2.9 - - + -
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Residues in contact with ASN 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ILE* 2.8 31.1 + - - +
35I ALA* 3.8 7.1 - - - +
37I LEU* 1.3 77.5 - - - +
39I GLU* 1.3 63.0 + - + +
41I GLY* 3.2 13.5 + - - -
42I VAL 4.7 3.4 - - - +
48I LYS* 3.4 35.2 - - + +
49I LEU* 2.8 54.2 + - - +
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Residues in contact with GLU 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590F ILE* 3.8 14.2 - - + +
593F LYS* 3.1 44.1 - - - +
594F ALA* 3.3 26.9 + - - +
597F LYS* 3.2 27.1 - - + +
35I ALA* 2.9 20.4 + - + +
36I PHE* 4.0 4.3 - - - +
38I ASN* 1.3 79.5 - - + +
40I ILE* 1.3 61.2 + - - +
41I GLY* 3.4 1.0 + - - -
30M ASP* 4.6 11.1 - - - +
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Residues in contact with ILE 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562F ARG* 3.2 28.9 + - + +
563F PHE* 3.7 32.8 - - + -
590F ILE* 4.3 15.9 - - + -
14I VAL* 3.8 38.1 - - + -
36I PHE* 3.0 26.4 + - + +
37I LEU* 3.3 29.8 - - + +
39I GLU* 1.3 76.5 - - - +
41I GLY* 1.3 56.9 + - - +
42I VAL* 4.2 8.3 - - + -
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Residues in contact with GLY 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562F ARG* 3.0 17.8 + - - -
37I LEU 3.2 4.4 + - - -
38I ASN 3.2 10.5 + - - -
39I GLU 3.1 4.1 - - - -
40I ILE* 1.3 75.6 - - - +
42I VAL* 1.3 65.1 + - - +
43I THR* 3.8 7.3 + - - -
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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