Contacts of the strand formed by residues 52 - 61 (chain C) in PDB entry 1PU5
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 LYS 52 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C PRO 4.1 1.2 - - - -
51C LEU* 1.3 74.1 - - - +
53C VAL* 1.3 62.1 + - - +
54C ASP* 3.7 34.7 + - - +
78C THR* 3.9 11.8 - - + +
79C PHE 3.4 10.1 - - - +
80C GLU* 4.1 20.1 - - + +
144C VAL 3.4 1.6 - - - +
145C LEU* 3.3 6.8 - - - +
146C SER* 2.8 53.2 + - - +
147C SER* 5.7 0.4 - - - -
149C GLY* 6.0 3.1 - - - +
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Residues in contact with VAL 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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51C LEU 4.0 0.2 + - - -
52C LYS* 1.3 74.8 - - - +
54C ASP* 1.3 62.5 + - - +
55C LEU* 3.7 31.2 - - + -
77C CYS 3.8 0.3 - - - +
78C THR* 3.2 3.6 - - - +
79C PHE* 2.8 47.2 + - + +
82C PHE* 3.7 41.7 - - + -
143C SER* 4.0 8.5 - - - +
144C VAL 3.4 3.8 - - - +
145C LEU* 3.8 20.0 - - + -
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Residues in contact with ASP 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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52C LYS* 3.7 24.3 + - - +
53C VAL* 1.3 72.5 - - - +
55C LEU* 1.3 61.8 + - - +
56C VAL* 5.6 2.5 - - + +
77C CYS 4.0 2.0 - - - -
78C THR* 2.8 37.7 + - - +
142C GLU 3.4 2.1 - - - +
143C SER* 3.4 2.9 - - - -
144C VAL* 2.9 54.3 + - + +
146C SER* 4.5 4.2 + - - -
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Residues in contact with LEU 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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53C VAL* 3.7 16.4 - - + -
54C ASP* 1.3 74.4 - - - +
56C VAL* 1.3 65.9 + - - +
67C LYS* 5.1 0.2 - - - -
75C GLY 4.2 13.5 - - - +
76C SER* 3.1 25.6 - - - +
77C CYS* 2.9 26.4 + - + +
78C THR* 4.7 1.3 + - - -
79C PHE* 4.1 18.6 - - + -
141C ILE* 4.4 21.8 - - + -
142C GLU 3.3 2.7 - - - +
143C SER* 3.1 36.3 - - - +
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Residues in contact with VAL 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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54C ASP* 5.6 2.7 - - + +
55C LEU* 1.3 78.3 - - - +
57C LEU* 1.3 59.0 + - - +
58C GLU* 4.1 28.9 - - + +
67C LYS* 4.0 32.5 - - + +
76C SER* 3.6 3.4 - - - -
140C ARG 3.8 1.0 - - - +
141C ILE* 3.2 6.2 - - - -
142C GLU* 2.9 53.2 + - + +
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Residues in contact with LEU 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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55C LEU 4.0 0.2 - - - -
56C VAL* 1.3 74.8 - - - +
58C GLU* 1.3 61.3 + - - +
67C LYS* 3.5 2.8 - - - -
68C ILE* 2.7 40.8 + - + -
74C ILE* 5.8 0.4 - - + -
75C GLY* 4.0 28.0 - - - +
76C SER* 2.8 16.2 + - - +
133C TRP* 3.5 33.4 - - + -
139C TYR* 4.4 17.0 - - + -
140C ARG 3.6 13.9 - - - +
141C ILE* 4.1 22.2 - - + -
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Residues in contact with GLU 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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56C VAL* 4.1 22.0 - - + +
57C LEU* 1.3 79.0 - - - +
59C LYS* 1.3 61.1 + - - +
65C TRP* 3.9 26.7 - - + +
66C ILE 3.2 6.7 - - - +
67C LYS* 3.8 19.3 + - + +
68C ILE* 4.5 1.6 - - - -
139C TYR* 3.3 10.1 - - - +
140C ARG* 2.5 80.5 + - + +
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Residues in contact with LYS 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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58C GLU* 1.3 75.3 - - - +
60C GLU* 1.3 74.8 + - - +
61C VAL* 3.4 12.2 + - + +
65C TRP* 3.7 3.4 - - - -
66C ILE* 2.9 33.9 + - + +
68C ILE* 4.1 17.4 - - + +
133C TRP* 3.0 26.1 + - + +
135C THR* 2.8 28.5 + - - +
136C THR 4.2 9.0 - - - -
137C GLY* 4.9 3.1 - - - -
138C ASN 3.6 7.6 - - - +
139C TYR* 3.6 32.8 - - + +
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Residues in contact with GLU 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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59C LYS* 1.3 80.7 - - - +
61C VAL* 1.3 65.7 + - - +
62C ALA 5.2 0.5 + - - -
63C GLY* 3.8 27.6 + - - +
64C LEU 3.3 9.6 - - - +
65C TRP* 3.6 27.3 - - + -
137C GLY* 5.8 0.9 - - - -
138C ASN* 2.8 55.4 + - + +
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Residues in contact with VAL 61 (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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59C LYS* 3.4 17.9 + - + +
60C GLU* 1.3 79.0 - - - +
62C ALA* 1.3 78.6 + - + +
63C GLY 3.2 0.4 - - - -
64C LEU* 2.7 28.3 + - - +
66C ILE* 3.8 30.2 - - + +
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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