Contacts of the helix formed by residues 54 - 60 (chain P) in PDB entry 1UW9
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 ASN 54 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55I GLU 5.5 1.6 + - - -
56I SER* 5.6 4.0 + - - +
58I ILE* 3.9 24.3 - - + +
59I ARG* 2.8 49.1 + - + +
226K TYR* 5.8 2.8 - - - -
229K GLN* 4.8 4.8 + - - +
52P VAL* 5.9 0.2 - - - +
53P SER* 1.3 83.4 - - - +
55P GLU* 1.3 65.3 - - - +
56P SER 3.2 2.9 - - - -
57P ALA* 3.0 20.0 + - + +
67P TYR* 5.7 2.0 - - - -
68P TYR* 3.9 7.8 - - - +
69P ASP* 3.5 3.1 - - - -
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Residues in contact with GLU 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 4.1 8.4 - - - +
54M ASN* 5.3 1.5 + - - -
49P LYS* 4.5 4.0 + - - -
53P SER* 2.4 33.9 + - - -
54P ASN* 1.3 75.9 - - - +
56P SER* 1.3 64.0 + - - +
57P ALA 3.2 0.5 + - - -
58P ILE* 3.3 23.9 + - - +
69P ASP* 3.2 7.4 + - - +
70P ASN* 4.6 3.5 + - - +
1141P EDO 2.7 39.9 + - - +
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Residues in contact with SER 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ASN* 5.4 5.6 + - - +
55P GLU* 1.3 72.3 - - - +
57P ALA* 1.3 55.8 + - - +
58P ILE* 3.0 7.4 - - - -
59P ARG* 2.9 32.8 + - - +
60P PHE* 3.9 6.0 - - - -
67P TYR* 3.4 17.9 + - - -
69P ASP* 2.7 33.3 + - - -
1141P EDO 4.0 6.8 - - - -
226R TYR* 3.5 29.9 - - - +
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Residues in contact with ALA 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 3.8 29.2 - - + +
59I ARG* 4.7 5.4 - - + +
54P ASN* 3.0 20.0 + - + +
56P SER* 1.3 75.8 - - - +
58P ILE* 1.3 61.3 + - - +
59P ARG 3.0 0.7 - - - -
60P PHE* 3.1 44.9 + - + +
64P SER* 4.4 12.3 - - - -
67P TYR* 4.8 3.7 - - + -
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Residues in contact with ILE 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 3.8 22.9 - - + +
54M ASN* 3.7 43.3 - - + +
55M GLU* 3.9 12.3 - - - +
57M ALA* 3.7 17.9 - - + +
58M ILE* 3.8 36.3 - - + +
64M SER* 5.3 0.2 - - - -
55P GLU 3.3 19.0 + - - +
56P SER 3.0 0.4 + - - -
57P ALA* 1.3 77.7 - - - +
59P ARG* 1.3 64.0 + - + +
60P PHE 3.3 3.8 + - - +
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Residues in contact with ARG 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ASN* 2.8 52.0 + - + +
57M ALA* 4.7 3.8 - - + +
62M SER* 5.8 2.8 - - - -
64M SER* 2.8 60.9 + - - +
66M LEU 4.0 1.4 - - - +
67M TYR* 2.8 24.5 + - - -
68M TYR* 3.5 22.7 - - - -
56P SER* 2.9 14.8 + - - +
58P ILE* 1.3 81.0 - - + +
60P PHE* 1.3 61.2 + - + +
226R TYR* 3.0 41.9 + - - +
229R GLN* 6.0 0.4 - - - -
258R LYS 5.1 0.5 - - - +
259R GLU 3.9 1.0 - - - +
260R LEU 4.3 1.6 - - - +
261R GLY* 2.9 26.8 + - - -
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Residues in contact with PHE 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M GLY 5.1 5.5 - - - +
62M SER* 5.4 2.9 - - - -
56P SER 3.9 12.3 - - - -
57P ALA* 3.1 31.9 + - + +
58P ILE 3.3 3.2 - - - +
59P ARG* 1.3 81.7 - - - +
61P GLY* 1.3 72.4 + - - +
63P VAL* 4.0 6.1 - - + -
64P SER* 4.0 17.9 - - - +
67P TYR* 3.5 59.0 - + + -
222R THR* 4.1 1.6 - - + -
226R TYR* 4.0 9.9 - + - -
259R GLU 3.1 3.1 - - - +
260R LEU* 3.3 46.2 - - + -
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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