Contacts of the helix formed by residues 51 - 65 (chain Y) in PDB entry 1XDM
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 THR 51 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU* 5.4 4.9 - - - +
49Y GLU* 4.1 8.8 - - - +
50Y ASN* 1.3 78.5 + - - +
52Y GLU* 1.3 71.5 + - + +
53Y GLU* 2.9 25.7 + - + +
54Y ASN* 2.9 32.3 + - - +
55Y ARG* 3.0 29.5 + - - +
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Residues in contact with GLU 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y THR* 1.3 77.5 - - + +
53Y GLU* 1.3 57.1 + - - +
55Y ARG* 3.4 30.7 + - - +
56Y ARG* 3.1 19.9 + - - -
81Y GLU* 4.0 10.6 - - + +
85Y GLN* 3.2 36.7 + - - +
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Residues in contact with GLU 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY 3.9 15.3 - - - +
316B LYS* 3.9 27.9 - - + +
317B ALA* 3.2 18.4 + - - +
51Y THR* 2.9 14.8 - - + +
52Y GLU* 1.3 76.6 - - - +
54Y ASN* 1.3 72.5 + - - +
55Y ARG 3.0 1.3 - - - -
56Y ARG* 2.7 49.0 + - - +
57Y GLN* 2.7 32.9 + - - +
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Residues in contact with ASN 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 5.6 1.9 - - - +
43Y LEU* 4.2 10.5 - - + +
48Y VAL* 4.2 12.2 - - + +
49Y GLU* 2.5 37.1 + - - +
51Y THR* 2.9 34.2 + - - +
53Y GLU* 1.3 77.2 - - - +
55Y ARG* 1.3 65.7 + - - +
57Y GLN* 3.7 7.0 - - - +
58Y PHE* 3.0 23.4 + - - +
313Y TRP* 3.7 10.2 - - + -
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Residues in contact with ARG 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y VAL* 3.8 29.4 - - - +
39Y MET* 3.5 38.4 - - + -
43Y LEU* 4.3 6.5 - - + -
50Y ASN* 2.8 34.6 - - - +
51Y THR* 3.0 18.8 + - - +
52Y GLU* 3.4 28.5 - - - +
53Y GLU 3.0 0.2 - - - -
54Y ASN* 1.3 77.9 - - - +
56Y ARG* 1.3 65.0 + - - +
57Y GLN 3.0 1.2 + - - -
58Y PHE* 3.8 3.2 - - - +
59Y ARG* 3.0 40.0 + - - +
79Y PHE* 6.2 0.2 - - - -
81Y GLU* 2.5 39.6 + - - +
85Y GLN* 5.1 0.2 - - - -
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Residues in contact with ARG 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ALA* 4.3 3.2 - - - +
318B ALA* 4.3 17.0 - - - +
52Y GLU* 3.1 6.6 + - - +
53Y GLU* 2.7 47.5 + - - +
55Y ARG* 1.3 75.3 - - - +
57Y GLN* 1.3 61.2 + - - +
59Y ARG* 3.9 1.7 - - - -
60Y GLU* 3.0 54.9 + - - +
85Y GLN* 3.0 41.8 - - + +
86Y LYS 2.8 28.5 + - - +
87Y ASP* 3.5 10.7 - - - +
88Y SER* 3.8 13.5 + - - +
93Y PHE* 3.3 15.3 - - + -
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Residues in contact with GLN 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLN* 4.0 13.1 + - - +
317B ALA* 3.5 28.9 - - - +
53Y GLU* 2.7 26.1 + - - +
54Y ASN* 3.7 7.0 - - - +
55Y ARG 3.0 0.6 + - - -
56Y ARG* 1.3 75.1 - - - +
58Y PHE* 1.3 58.0 + - - +
60Y GLU* 2.5 43.1 + - - +
61Y ILE* 2.8 20.5 + - + +
88Y SER* 5.7 0.2 - - - +
313Y TRP* 3.9 19.6 + - + -
315Y GLY 4.9 1.9 - - - +
317Y ALA* 3.7 24.1 + - - +
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Residues in contact with PHE 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Y MET* 4.6 10.1 - - + -
43Y LEU* 5.1 1.8 - - + -
54Y ASN 3.0 14.8 + - - +
55Y ARG* 3.8 3.4 - - - +
57Y GLN* 1.3 75.7 - - - +
59Y ARG* 1.3 66.2 + - + +
61Y ILE* 2.8 30.0 + - + +
62Y LEU* 3.0 32.6 + - + +
306Y GLN* 3.5 29.8 - - + -
309Y ALA 3.4 21.5 - - - -
310Y LEU* 3.3 47.1 - - + -
313Y TRP* 3.6 32.6 - + + -
323Y THR* 3.9 12.8 - - + -
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Residues in contact with ARG 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Y ALA* 3.6 31.0 + - + -
34Y GLU* 3.3 24.0 + - - +
35Y SER 5.4 0.2 - - - -
36Y VAL 5.4 0.2 - - - +
39Y MET* 3.0 44.1 - - - +
55Y ARG* 3.0 25.3 + - - +
56Y ARG* 4.3 3.4 - - - +
58Y PHE* 1.3 86.6 - - + +
60Y GLU* 1.3 61.3 + - - +
62Y LEU* 3.7 14.9 - - + +
63Y PHE* 3.1 43.8 + - + -
79Y PHE* 4.3 6.7 - - - +
81Y GLU* 3.8 8.6 + - - -
82Y THR* 2.5 45.4 + - - +
93Y PHE* 4.6 4.5 - - + -
306Y GLN* 5.5 2.0 + - - +
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Residues in contact with GLU 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y ARG* 3.0 29.5 + - - +
57Y GLN* 2.5 28.6 + - - +
59Y ARG* 1.3 69.8 - - - +
61Y ILE* 1.3 53.4 + - + +
63Y PHE* 3.7 1.0 - - - +
64Y SER* 2.8 42.9 + - - -
87Y ASP* 3.2 21.5 - - + +
88Y SER* 2.3 51.5 + - - -
89Y GLN* 4.6 1.6 - - - +
93Y PHE* 3.5 13.6 - - + -
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Residues in contact with ILE 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Y GLN* 2.8 18.5 + - + +
58Y PHE* 2.8 14.4 + - - +
60Y GLU* 1.3 77.0 - - + +
62Y LEU* 1.3 70.6 + - - +
64Y SER* 3.2 15.5 + - - -
65Y VAL 3.2 7.6 + - - -
313Y TRP* 3.3 44.0 - - + +
317Y ALA* 5.9 1.1 - - - -
320Y LYS* 3.9 27.6 - - + +
323Y THR* 3.5 25.8 - - + -
324Y GLN* 3.4 23.6 - - + +
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Residues in contact with LEU 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y LEU* 4.9 9.2 - - + -
32Y ALA* 5.1 4.5 - - + -
58Y PHE* 3.0 48.9 + - + +
59Y ARG* 3.7 18.6 - - + +
61Y ILE* 1.3 77.6 - - - +
63Y PHE* 1.3 62.5 + - + +
64Y SER 2.7 0.5 + - - -
65Y VAL* 2.7 40.1 + - - +
306Y GLN* 4.0 22.2 - - + +
309Y ALA* 4.4 5.8 - - + -
323Y THR* 4.6 4.9 - - + -
324Y GLN* 5.3 1.1 - - - -
327Y PHE* 3.9 45.5 - - + -
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Residues in contact with PHE 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y LEU* 4.1 9.6 - - + -
32Y ALA* 3.7 17.0 - - + -
59Y ARG* 3.1 30.3 + - + +
60Y GLU 4.2 1.8 - - - +
62Y LEU* 1.3 84.6 - - + +
64Y SER* 1.3 56.6 + - - +
65Y VAL* 3.3 2.0 - - - -
76Y VAL* 3.5 22.0 - - + -
78Y LEU* 3.2 34.8 - - + -
82Y THR* 4.3 4.3 - - + -
93Y PHE* 3.7 34.8 - + + -
96Y ILE* 3.6 13.2 - - + +
97Y LEU* 3.7 31.0 - - + +
100Y LYS* 3.1 27.9 - - - +
327Y PHE* 5.8 0.7 - + - -
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Residues in contact with SER 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Y GLU* 2.8 28.0 + - - -
61Y ILE* 3.2 5.5 + - - -
62Y LEU 2.7 3.0 + - - -
63Y PHE* 1.3 71.0 - - - +
65Y VAL* 1.3 70.1 + - - +
66Y ASP* 4.4 0.7 - - - +
87Y ASP* 6.2 0.7 - - - -
96Y ILE* 5.2 7.0 - - - -
100Y LYS* 4.5 5.5 + - - +
320Y LYS* 3.2 19.5 + - - -
324Y GLN* 3.1 18.5 + - - -
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Residues in contact with VAL 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Y ILE 3.2 2.2 + - - -
62Y LEU 2.7 17.8 + - - +
63Y PHE* 4.9 2.0 - - - -
64Y SER* 1.3 85.8 - - - +
66Y ASP* 1.3 74.2 + - + +
67Y SER 3.5 0.3 + - - -
69Y ILE* 3.5 39.0 - - + -
100Y LYS* 3.6 13.5 + - - -
324Y GLN* 3.1 37.2 - - + +
327Y PHE* 4.0 9.4 - - + -
328Y MET* 3.2 30.3 - - + -
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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