Contacts of the helix formed by residues 44 - 60 (chain C) in PDB entry 2XXA
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 ALA 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C ASP 4.0 1.8 + - - -
43C VAL* 1.4 74.4 - - - +
45C LEU* 1.4 59.4 + - - +
46C PRO* 3.5 5.6 - - + -
47C VAL* 3.1 17.0 - - + +
48C VAL* 3.0 24.8 + - - +
226C GLY 5.5 0.6 + - - +
227C GLN* 3.4 23.4 - - - +
230C ALA* 3.9 28.9 - - + +
261C SER* 3.2 16.2 + - - +
265C ILE* 5.5 1.1 - - + -
42D ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 4.3 14.4 - - - +
39C LEU* 4.3 17.7 - - + -
43C VAL 3.9 0.6 + - - -
44C ALA* 1.4 67.5 - - - +
46C PRO* 1.4 67.7 - - + +
48C VAL* 3.1 9.4 + - + -
49C ARG* 2.8 64.7 + - + +
227C GLN* 3.2 16.0 + - - +
38D GLU* 3.3 44.4 - - + +
41D LEU* 3.8 21.3 - - + -
42D ILE* 3.9 16.4 - - + +
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Residues in contact with PRO 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ALA* 3.6 12.6 - - + -
45C LEU* 1.4 92.0 - - + +
47C VAL* 1.4 55.7 + - - +
49C ARG* 4.4 13.4 - - + +
50C GLU* 3.3 29.5 + - - +
230C ALA* 4.9 8.3 - - + -
234C LYS* 4.9 15.9 - - - +
264C HIS* 4.7 2.1 + - - -
265C ILE* 5.8 7.2 - - + -
42D ILE* 4.5 13.0 - - + -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.8 20.0 - - + -
44C ALA* 3.1 34.1 - - + +
46C PRO* 1.4 74.9 - - - +
48C VAL* 1.4 58.8 + - - +
50C GLU* 3.5 1.4 + - - +
51C PHE* 3.0 33.1 + - + +
260C LEU* 4.0 17.7 - - + +
261C SER* 3.9 13.9 - - - +
264C HIS* 3.7 46.6 + - + +
265C ILE* 5.2 5.4 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 4.2 17.9 - - + +
38C LEU* 4.1 27.7 - - + +
39C LEU* 5.0 11.2 - - + +
43C VAL* 3.6 31.9 - - + +
44C ALA 3.0 21.0 + - - +
45C LEU* 3.8 9.0 - - + +
47C VAL* 1.4 74.9 - - - +
49C ARG* 1.4 60.0 + - + +
51C PHE* 3.3 6.4 + - - +
52C ILE* 3.1 49.7 + - + +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 5.1 5.8 - - - +
45C LEU* 2.8 49.2 + - + +
46C PRO* 4.4 11.2 - - + +
48C VAL* 1.4 72.9 - - + +
50C GLU* 1.4 60.5 + - - +
52C ILE* 3.7 13.2 + - + +
53C ASN* 3.7 17.5 + - - +
38D GLU* 3.4 41.1 + - - +
42D ILE* 6.0 1.6 - - - +
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PRO 3.3 18.9 + - - +
47C VAL 4.0 2.9 - - - +
48C VAL 3.4 0.6 - - - -
49C ARG* 1.4 75.6 - - - +
51C PHE* 1.4 59.0 + - - +
52C ILE 3.4 0.2 - - - -
53C ASN* 3.7 8.4 + - + +
54C ARG* 3.2 26.1 + - - +
264C HIS* 3.2 33.5 + - + +
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Residues in contact with PHE 51 (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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38C LEU* 5.0 15.3 - - + -
47C VAL* 3.0 23.6 + - + +
48C VAL* 3.3 6.3 + - - +
50C GLU* 1.4 75.7 - - - +
52C ILE* 1.4 64.2 + - + +
54C ARG* 3.4 40.6 + - - +
55C VAL* 3.1 43.7 + - + +
78C VAL* 4.1 13.0 - - + -
81C GLU* 3.8 34.8 - - + -
82C LEU* 3.7 30.5 - - + -
85C ALA* 4.3 6.3 - - + -
260C LEU* 5.3 9.4 - - + -
264C HIS* 5.6 4.7 - + + -
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Residues in contact with ILE 52 (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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31C LEU* 3.8 25.4 - - + +
34C VAL* 6.5 0.7 - - + -
35C ARG* 3.8 40.4 - - + +
38C LEU* 5.7 6.1 - - + -
48C VAL* 3.1 32.0 + - + +
49C ARG* 3.9 11.9 - - + +
50C GLU 3.4 0.2 - - - -
51C PHE* 1.4 74.4 - - + +
53C ASN* 1.4 59.4 + - - +
55C VAL* 3.4 8.1 + - - +
56C LYS* 3.2 50.6 + - - +
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Residues in contact with ASN 53 (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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49C ARG 3.7 9.0 + - - +
50C GLU* 3.7 10.7 + - - +
51C PHE 3.4 0.2 - - - -
52C ILE* 1.4 76.0 - - - +
54C ARG* 1.4 63.3 + - - +
56C LYS* 3.5 19.5 + - - +
57C GLU* 3.5 38.5 + - - +
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Residues in contact with ARG 54 (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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50C GLU* 3.2 17.6 + - - +
51C PHE* 3.5 31.6 - - + +
52C ILE 3.3 0.2 - - - -
53C ASN* 1.4 77.1 - - - +
55C VAL* 1.4 61.8 + - + +
57C GLU* 3.9 12.8 + - - +
58C LYS* 3.8 18.4 - - + +
81C GLU* 3.6 29.7 + - + +
84C ALA* 5.2 3.2 - - - +
85C ALA* 3.5 37.9 - - - +
264C HIS* 4.6 18.4 + - - -
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Residues in contact with VAL 55 (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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31C LEU* 5.2 9.4 - - + -
51C PHE* 3.1 41.2 + - + +
52C ILE* 3.7 7.0 - - - +
53C ASN 3.4 0.2 - - - -
54C ARG* 1.4 75.3 - - + +
56C LYS* 1.4 54.4 + - + +
58C LYS* 3.1 5.9 + - - +
59C ALA* 2.8 38.3 + - + +
74C PHE* 4.9 8.3 - - + -
77C ILE* 4.1 21.5 - - + +
78C VAL* 4.0 35.0 - - + -
81C GLU* 5.1 4.5 - - + -
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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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24C GLU* 5.4 18.4 - - + +
27C VAL* 5.7 6.7 - - + -
31C LEU* 4.2 18.2 - - + +
52C ILE* 3.2 38.4 + - + +
53C ASN* 3.6 23.7 + - - +
54C ARG 3.5 0.4 - - - -
55C VAL* 1.4 76.2 - - + +
57C GLU* 1.4 60.9 + - + +
58C LYS 3.5 0.5 + - - -
59C ALA* 4.4 5.4 - - - -
60C VAL* 3.5 30.2 + - + +
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Residues in contact with GLU 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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53C ASN* 3.5 31.2 + - - +
54C ARG* 4.1 11.0 - - - +
55C VAL 3.3 0.8 - - - -
56C LYS* 1.4 76.1 - - + +
58C LYS* 1.3 62.1 + - + +
60C VAL* 5.5 0.2 - - - +
61C GLY* 3.9 16.0 + - - -
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Residues in contact with LYS 58 (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 ARG* 3.8 13.7 - - + +
55C VAL* 3.1 7.4 + - - +
57C GLU* 1.3 80.0 - - + +
59C ALA* 1.4 62.2 + - - +
60C VAL 3.5 0.6 + - - -
61C GLY* 3.8 6.4 + - - +
63C GLU* 3.0 44.8 - - - +
77C ILE* 3.8 16.6 - - + -
81C GLU* 3.6 33.2 + - + +
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Residues in contact with ALA 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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22C LEU* 3.3 28.0 - - + +
27C VAL* 5.2 9.6 - - + -
55C VAL* 2.8 29.5 + - + +
56C LYS* 3.7 7.4 + - - +
57C GLU 3.7 0.2 - - - -
58C LYS* 1.4 72.9 - - - +
60C VAL* 1.3 63.1 + - + +
63C GLU 3.2 22.9 - - - +
74C PHE* 5.3 4.3 - - + -
77C ILE* 3.8 16.5 - - + +
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Residues in contact with VAL 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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21C ARG* 5.3 7.5 - - + +
22C LEU 3.3 23.5 - - - +
23C THR* 4.4 20.0 - - + -
24C GLU* 5.2 9.2 - - + +
27C VAL* 6.1 1.8 - - + -
56C LYS* 3.5 19.5 + - + +
57C GLU 5.8 0.2 - - - -
58C LYS 3.5 0.2 - - - -
59C ALA* 1.3 77.8 - - + +
61C GLY* 1.3 53.5 + - - +
62C HIS* 2.8 18.2 + - - -
63C GLU 4.2 0.9 + - - -
64C VAL* 4.6 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