Contacts of the helix formed by residues 50 - 61 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B VAL 5.3 0.4 - - - +
48B ASN 4.1 1.0 - - - -
49B GLN* 1.3 74.8 - - - +
51B ILE* 1.3 66.7 + - - +
52B VAL* 3.0 5.8 + - - +
53B SER* 2.8 24.5 + - - -
54B MET* 3.0 27.7 + - - +
82B VAL* 4.9 4.7 - - + +
140B THR* 5.7 0.4 - - - -
353B PHE* 4.9 9.0 - - + -
374B LEU* 3.9 11.7 - - + +
382B ARG* 2.9 33.8 + - - +
384B TYR* 2.6 35.3 + - - -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 1.3 74.3 - - - +
52B VAL* 1.3 63.8 + - + +
54B MET* 4.1 6.7 - - + -
55B GLY* 3.0 15.6 + - - -
78B THR* 4.1 13.2 - - + +
80B SER* 3.6 41.1 - - - +
81B ALA* 3.9 14.6 - - - -
82B VAL* 4.1 19.7 - - + +
88B ALA* 4.1 23.6 - - + -
92B ILE* 4.5 1.0 - - - +
138B THR* 2.8 47.5 + - + +
139B ASP* 4.2 7.0 - - - -
140B THR* 4.6 6.0 - - + +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 3.0 3.2 + - - +
51B ILE* 1.3 80.1 - - + +
53B SER* 1.3 61.3 + - - +
55B GLY* 3.3 1.6 + - - -
56B ALA* 3.0 26.9 + - - +
82B VAL* 4.6 6.1 - - + -
88B ALA* 4.1 18.6 - - + -
91B GLN* 3.9 35.0 - - + +
92B ILE* 3.8 14.4 - - + +
95B LEU* 3.8 20.2 - - + -
384B TYR* 3.3 36.6 - - + +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASN 3.8 0.3 + - - -
49B GLN* 2.8 26.9 + - - -
50B ASP* 2.8 34.6 + - - -
52B VAL* 1.3 76.3 - - - +
54B MET* 1.3 56.2 + - - +
56B ALA* 3.8 1.8 - - - +
57B ASN* 2.9 34.7 + - - -
95B LEU* 5.4 0.2 - - - -
372B PHE* 3.7 11.2 - - - -
373B TYR* 3.7 25.1 - - - -
374B LEU 4.2 0.2 - - - -
384B TYR* 4.2 9.4 - - - -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TYR* 3.8 20.3 - - + +
13B PRO* 4.4 13.2 - - - -
45B SER* 5.2 1.8 - - - -
49B GLN* 3.8 25.4 - - + +
50B ASP 3.0 23.2 + - - +
51B ILE* 4.1 3.8 - - - -
53B SER* 1.3 76.8 + - - +
55B GLY* 1.3 63.5 + - - +
57B ASN* 3.3 2.8 + - - +
58B ALA* 3.1 18.5 + - - +
138B THR* 3.8 17.5 - - - +
139B ASP 3.5 24.7 - - - +
140B THR* 4.0 17.5 - - + -
155B ALA* 4.3 6.5 - - - -
156B GLY* 3.7 22.7 - - - +
157B ALA* 3.5 14.6 - - + +
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE 3.0 18.0 + - - -
52B VAL 3.8 1.3 - - - -
54B MET* 1.3 77.8 - - - +
56B ALA* 1.3 61.9 + - - +
58B ALA* 3.3 3.6 + - - +
59B ALA* 3.1 23.9 + - - +
92B ILE* 4.2 3.6 - - - -
136B ILE* 3.7 32.6 - - - +
138B THR* 4.4 0.2 - - - -
157B ALA* 3.8 7.5 - - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL 3.0 17.2 + - - +
53B SER 3.8 3.1 - - - +
54B MET 3.3 0.2 - - - -
55B GLY* 1.3 76.4 - - - +
57B ASN* 1.3 57.1 + - - +
59B ALA* 3.3 0.7 + - - -
60B LYS* 2.8 33.4 + - - +
92B ILE* 4.3 13.7 - - + +
95B LEU* 4.2 18.6 - - + -
96B LEU* 3.9 8.5 - - + +
372B PHE* 3.6 30.5 - - + -
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN* 4.2 1.7 + - - -
11B TYR* 3.6 38.0 - - + +
49B GLN* 3.4 12.9 + - - +
53B SER 2.9 19.7 + - - +
54B MET 3.7 0.4 - - - +
56B ALA* 1.3 78.3 - - - +
58B ALA* 1.3 60.9 + - - +
60B LYS* 3.6 25.4 - - - +
61B ASP* 4.2 9.5 + - - +
371B ILE* 3.4 12.5 - - - +
372B PHE* 2.8 52.8 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN* 2.8 34.5 + - - +
10B PHE* 4.1 2.0 - - - -
11B TYR* 3.8 11.6 - - - +
54B MET 3.1 16.4 + - - +
55B GLY 3.7 4.7 - - - +
56B ALA 3.3 0.2 - - - -
57B ASN* 1.3 78.2 - - - +
59B ALA* 1.3 62.0 + - - +
62B ILE* 4.1 1.4 - - - +
136B ILE* 5.5 0.2 - - + -
157B ALA* 3.6 28.3 - - + +
158B VAL 4.3 0.2 - - - -
159B ALA* 3.7 20.0 - - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY 3.1 14.8 + - - +
56B ALA 4.0 0.7 - - - +
58B ALA* 1.3 77.7 - - - +
60B LYS* 1.3 65.7 + - - +
61B ASP 3.2 2.5 - - - -
62B ILE* 3.0 21.2 + - - +
63B ILE* 3.5 11.5 - - + +
96B LEU* 3.8 24.9 - - + -
134B LEU* 4.1 10.5 - - + -
136B ILE* 4.0 8.5 - - + -
159B ALA* 3.6 17.7 - - + +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA 2.8 16.3 + - - +
57B ASN* 3.6 39.3 - - - +
59B ALA* 1.3 72.6 - - - +
61B ASP* 1.3 84.9 + - - +
62B ILE 3.3 1.0 + - - -
63B ILE* 3.6 23.9 + - - +
96B LEU* 4.1 7.3 - - + +
370B HIS* 3.6 23.8 + - - +
371B ILE* 4.2 9.3 - - - +
372B PHE* 3.9 22.9 - - + -
387B PRO* 4.2 7.1 - - + +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 5.4 1.6 + - - -
9B ASN* 4.0 22.3 + - - +
57B ASN 4.2 5.4 - - - +
58B ALA 4.4 1.4 + - - -
59B ALA 3.1 1.2 + - - -
60B LYS* 1.3 108.0 + - - +
62B ILE* 1.3 62.6 + - + +
63B ILE 3.6 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