Contacts of the helix formed by residues 50 - 61 (chain D) in PDB entry 1XPM
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 ASP 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D VAL 5.4 0.4 - - - +
48D ASN 4.0 1.6 - - - -
49D GLN* 1.3 73.7 - - - +
51D ILE* 1.3 66.8 + - - +
52D VAL* 3.0 5.2 + - - +
53D SER* 2.8 26.8 + - - -
54D MET* 3.0 27.7 + - - +
82D VAL* 4.9 4.8 - - + +
140D THR* 5.7 0.2 - - - -
353D PHE* 4.9 10.5 - - + -
374D LEU* 3.8 11.6 - - + +
382D ARG* 3.0 31.7 + - - +
384D TYR* 2.5 34.3 + - - -
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASP* 1.3 73.7 - - + +
52D VAL* 1.3 64.6 + - + +
54D MET* 4.2 6.3 - - + -
55D GLY* 3.1 16.1 + - - -
78D THR* 4.1 12.6 - - + +
80D SER* 3.6 40.8 - - - +
81D ALA* 4.0 14.1 - - - -
82D VAL* 4.1 18.8 - - + +
88D ALA* 4.0 22.9 - - + -
92D ILE* 4.4 0.9 - - - +
106D GLU* 5.0 0.4 - - - +
138D THR* 2.8 48.7 + - + +
139D ASP* 4.1 7.2 - - - +
140D THR* 4.7 5.8 - - + +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ASP* 3.0 2.8 + - - +
51D ILE* 1.3 80.4 - - + +
53D SER* 1.3 65.9 + - - +
55D GLY 3.3 0.9 + - - -
56D ALA* 3.0 22.5 + - - +
82D VAL* 4.9 5.8 - - + -
88D ALA* 4.0 18.8 - - + +
91D GLN* 3.8 36.8 - - + +
92D ILE* 3.8 13.9 - - + +
95D LEU* 3.7 22.4 - - + -
384D TYR* 3.3 35.4 - - + +
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Residues in contact with SER 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ASN 3.7 0.3 + - - -
49D GLN* 2.9 25.7 + - - -
50D ASP* 2.8 35.0 + - - -
52D VAL* 1.3 77.2 - - - +
54D MET* 1.3 56.1 + - - +
56D ALA* 3.4 2.6 + - - +
57D ASN* 2.9 35.8 + - - -
95D LEU* 5.3 0.4 - - - -
372D PHE* 3.8 9.9 - - - -
373D TYR* 3.7 30.7 - - - -
374D LEU 4.2 0.4 - - - -
384D TYR* 4.2 4.9 - - - -
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Residues in contact with MET 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 3.8 18.4 - - + +
13D PRO* 4.4 13.5 - - - -
45D SER* 5.2 1.8 - - - -
49D GLN* 3.7 24.7 - - + +
50D ASP 3.0 22.3 + - - +
51D ILE* 4.2 3.6 - - - -
53D SER* 1.3 77.9 + - - +
55D GLY* 1.3 62.7 + - - +
57D ASN* 3.3 2.9 + - - +
58D ALA* 3.0 18.5 + - - +
138D THR* 3.9 14.4 - - - +
139D ASP 3.4 25.8 - - - +
140D THR* 3.9 17.9 - - + -
155D ALA* 4.3 5.2 - - - -
156D GLY* 3.7 27.6 - - - +
157D ALA* 3.5 15.8 - - + +
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Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE 3.1 18.4 + - - -
52D VAL 3.8 0.7 - - - -
54D MET* 1.3 76.8 - - - +
56D ALA* 1.3 60.0 + - - +
58D ALA* 3.3 3.6 + - - +
59D ALA* 3.1 23.6 + - - +
92D ILE* 4.1 4.0 - - - -
136D ILE* 3.7 33.0 - - - +
138D THR* 4.4 0.2 - - - -
157D ALA* 3.8 6.6 - - - +
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL 3.0 16.8 + - - +
53D SER 3.8 2.7 - - - +
55D GLY* 1.3 75.9 - - - +
57D ASN* 1.3 57.6 + - - +
59D ALA* 3.3 0.4 + - - -
60D LYS* 2.9 33.6 + - - +
92D ILE* 4.2 15.0 - - + +
95D LEU* 4.2 16.8 - - + -
96D LEU* 3.9 9.9 - - + +
372D PHE* 3.6 29.6 - - + -
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASN* 4.2 1.9 + - - -
10D PHE 5.3 0.2 - - - +
11D TYR* 3.6 37.5 - - + +
49D GLN* 3.4 13.1 + - - +
53D SER 2.9 19.9 + - - +
54D MET 3.7 0.7 - - - +
56D ALA* 1.3 77.3 - - - +
58D ALA* 1.3 62.0 + - - +
60D LYS* 3.6 22.5 - - - +
61D ASP* 4.1 9.0 - - - +
371D ILE* 3.4 13.7 - - - +
372D PHE* 2.8 52.7 + - - +
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ASN* 2.8 34.6 + - - +
10D PHE 4.1 1.8 - - - -
11D TYR* 3.8 11.4 - - - +
54D MET 3.0 16.1 + - - +
55D GLY* 3.7 5.2 - - - +
56D ALA 3.2 0.4 - - - -
57D ASN* 1.3 75.9 - - - +
59D ALA* 1.3 59.9 + - - +
62D ILE* 4.2 1.2 - - - +
157D ALA* 3.6 30.5 - - + +
158D VAL 4.3 0.4 - - - -
159D ALA* 3.6 18.9 - - + +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 3.1 15.8 + - - +
56D ALA 4.0 0.2 - - - +
58D ALA* 1.3 77.7 - - - +
60D LYS* 1.3 65.1 + - - +
61D ASP 3.2 3.1 - - - -
62D ILE* 3.0 16.3 + - - +
63D ILE* 3.2 16.7 - - + +
96D LEU* 3.8 24.2 - - + -
134D LEU* 4.2 11.2 - - + -
136D ILE* 4.0 8.7 - - + -
159D ALA* 3.6 17.0 - - + -
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA 2.9 12.5 + - - +
57D ASN* 3.6 31.2 - - - +
59D ALA* 1.3 76.3 - - - +
61D ASP* 1.3 91.6 + - - +
62D ILE 3.4 0.7 + - - -
63D ILE* 3.7 17.0 + - - +
96D LEU* 4.1 10.7 - - + +
370D HIS* 3.7 23.8 + - - +
371D ILE* 4.2 8.6 - - - +
372D PHE* 3.9 27.6 - - + -
387D PRO* 4.3 7.3 - - + +
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Residues in contact with ASP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LYS* 5.7 0.3 - - - -
9D ASN* 4.1 21.5 + - - +
57D ASN 4.1 6.6 - - - +
58D ALA 4.5 1.2 + - - -
59D ALA 3.1 1.4 + - - -
60D LYS* 1.3 106.1 + - - +
62D ILE* 1.3 64.4 + - + +
63D ILE 3.6 0.4 - - - -
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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