Contacts of the helix formed by residues 55 - 66 (chain C) in PDB entry 2L9H
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 LYS 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C ILE 6.2 0.2 - - - +
16C ALA 5.6 6.4 + - - -
52C ASN* 3.0 36.3 + - + +
54C GLU* 1.3 74.4 - - - +
56C LYS* 1.3 64.5 + - - +
57C TRP* 3.9 21.1 - - + +
58C VAL* 3.2 21.7 + - + +
59C ARG* 2.5 25.9 + - - -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU 3.6 2.6 + - - -
55C LYS* 1.3 73.1 - - - +
57C TRP* 1.3 65.0 + - - +
59C ARG* 3.2 11.2 + - - +
60C GLU* 2.6 67.0 + - + +
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Residues in contact with TRP 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.7 31.9 + - + -
16C ALA 5.2 3.0 + - - -
17C ARG* 3.9 3.2 - - - +
18C PRO* 3.4 47.9 - - + +
19C LEU* 3.8 10.8 - - + -
41C PHE* 3.6 33.7 - + - -
51C ALA* 4.1 2.2 - - + -
52C ASN 5.6 0.4 - - - -
55C LYS* 3.9 25.0 - - + +
56C LYS* 1.3 80.1 - - - +
58C VAL* 1.3 70.6 + - + +
60C GLU* 3.6 13.2 - - - +
61C TYR* 2.9 70.0 + + + -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.7 37.2 - - + -
41C PHE* 4.1 4.0 - - + -
51C ALA* 3.9 8.3 - - + -
52C ASN 3.0 31.6 - - - +
53C PRO* 4.0 8.1 - - + -
55C LYS* 3.4 15.7 - - + +
56C LYS 3.1 0.6 - - - -
57C TRP* 1.3 106.8 - - + +
59C ARG* 1.3 62.7 + - - +
61C TYR* 3.4 2.4 + - - +
62C ILE* 3.1 29.9 + - + +
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PRO* 2.7 26.5 + - - -
54C GLU* 2.6 35.5 + - - +
55C LYS 2.5 35.6 + - - -
56C LYS* 3.2 12.5 + - - +
58C VAL* 1.3 80.3 - - - +
60C GLU* 1.3 58.9 + - + +
62C ILE* 3.3 14.6 - - + +
63C ASN* 3.0 40.7 + - - +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 2.6 63.1 + - + +
57C TRP* 3.6 13.6 - - - +
59C ARG* 1.3 75.2 - - + +
61C TYR* 1.3 71.3 + - + +
63C ASN* 3.2 8.7 + - - +
64C SER* 2.9 24.0 + - - -
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Residues in contact with TYR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PRO* 3.9 9.6 - - + +
19C LEU 2.5 29.1 + - - -
20C PRO* 4.5 0.3 - - - +
21C ARG* 3.5 35.4 + - + +
24C ILE* 3.4 31.0 - - + -
41C PHE* 3.8 12.3 - + + -
57C TRP* 2.9 56.8 + + + +
58C VAL 3.6 4.9 - - - +
59C ARG 3.4 0.2 - - - -
60C GLU* 1.3 81.0 - - + +
62C ILE* 1.3 58.1 + - - +
64C SER* 3.2 7.1 + - - -
65C LEU* 2.8 37.7 + - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.0 21.5 - - - +
29A TYR* 3.5 32.5 - - + +
27C TYR* 2.8 61.7 - - + +
29C TYR* 5.7 0.9 - - + -
39C VAL* 3.9 18.4 - - + -
41C PHE* 4.7 2.5 - - + -
53C PRO* 5.8 0.9 - - + -
58C VAL* 3.1 21.9 + - + +
59C ARG* 3.3 22.9 - - + +
61C TYR* 1.3 73.2 - - - +
63C ASN* 1.3 68.0 + - - +
65C LEU* 3.2 10.6 + - - +
66C GLU 3.2 0.7 + - - -
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Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 4.6 2.9 + - - -
8A THR* 5.1 2.9 - - - +
9A PRO* 6.1 0.3 - - - +
28A PHE* 3.4 16.2 - - + -
29A TYR* 3.2 19.8 + - - +
30A THR 4.3 1.0 + - - -
31A SER* 3.2 37.9 + - - +
59C ARG* 3.0 26.3 + - - +
60C GLU* 3.2 10.9 + - - +
62C ILE* 1.3 85.1 - - - +
64C SER* 1.3 61.5 + - - +
67C MET* 3.4 32.4 + - + +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 3.0 31.3 + - - -
60C GLU 2.9 12.1 + - - -
61C TYR* 3.5 8.5 - - - -
62C ILE 3.1 0.2 - - - -
63C ASN* 1.3 76.2 - - - +
65C LEU* 1.3 65.2 + - - +
67C MET* 3.0 30.1 + - - +
68C SER* 3.4 8.0 + - - -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 5.1 0.7 + - - -
26A GLU* 5.0 2.9 - - + +
27A TYR 4.8 0.7 - - - +
21C ARG* 3.2 36.8 - - - +
24C ILE* 3.7 25.1 - - + +
25C LYS 4.3 11.4 - - - +
26C GLU* 4.3 4.0 - - - -
27C TYR* 3.5 42.2 - - + -
41C PHE* 3.9 13.2 - - + -
61C TYR* 2.8 25.1 + - + +
62C ILE 3.2 4.9 + - - +
64C SER* 1.3 72.3 - - - +
66C GLU* 1.3 70.4 + - - +
68C SER* 2.8 19.5 + - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 2.9 15.1 + - - -
26A GLU* 2.8 13.8 - - - +
27A TYR 2.6 25.9 + - - +
28A PHE* 2.7 61.0 - - + +
40A VAL* 3.6 12.6 - - + +
42A VAL* 2.3 48.8 - - + +
48A GLN* 3.2 14.9 + - - +
62C ILE 3.2 1.4 + - - -
64C SER 3.3 0.4 - - - -
65C LEU* 1.3 79.8 - - - +
67C MET* 1.3 58.9 + - - +
68C SER 3.7 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