Contacts of the strand formed by residues 58 - 62 (chain C) in PDB entry 1UUG
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 VAL 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C VAL* 4.3 0.4 - - - +
57C LYS* 1.3 91.2 - - + +
59C VAL* 1.3 64.2 + - - +
60C ILE* 4.2 8.1 - - + -
118C GLY 3.2 2.5 + - - +
119C VAL* 3.3 17.3 - - + +
120C LEU* 2.8 31.9 + - - +
160C VAL* 3.3 23.8 - - + +
162C LEU* 4.1 26.9 - - + -
206C ALA* 4.5 12.8 - - + -
210C LEU* 4.5 12.8 - - + -
218C ILE* 4.5 9.9 - - + -
220C TRP* 4.6 6.7 - - + -
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Residues in contact with VAL 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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56C VAL* 3.6 27.4 - - + -
58C VAL* 1.3 73.5 - - - +
60C ILE* 1.3 69.0 + - - +
61C LEU* 4.2 23.6 - - + -
120C LEU* 3.6 22.2 - - + +
122C LEU* 5.0 2.9 - - + -
149C ILE* 6.1 0.9 - - + -
152C ILE* 4.2 13.0 - - + -
159C VAL* 3.9 12.6 - - + -
160C VAL 2.8 9.5 + - - +
161C PHE* 3.6 31.1 - - + -
162C LEU* 2.9 26.5 + - - +
163C LEU* 5.6 1.0 - - + +
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Residues in contact with ILE 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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58C VAL* 4.2 5.8 - - + -
59C VAL* 1.3 79.2 - - - +
61C LEU* 1.3 65.7 + - - +
62C GLY 3.9 0.2 + - - -
76C ALA* 4.6 1.4 - - - +
77C PHE* 3.9 20.6 - - + -
92C MET* 5.4 0.4 - - + -
114C TRP* 4.4 14.6 - - + -
119C VAL* 4.0 20.0 - - + -
120C LEU 3.0 6.5 + - - +
121C LEU* 3.8 18.1 - - + -
122C LEU 3.3 23.2 + - - +
162C LEU* 3.9 32.8 - - + +
164C TRP* 3.9 33.7 - - + -
203C PHE* 4.9 1.3 - - + -
220C TRP* 4.8 5.8 - - + -
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Residues in contact with LEU 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 VAL* 4.2 16.4 - - + -
60C ILE* 1.3 74.4 - - - +
62C GLY* 1.3 62.5 + - - +
77C PHE* 3.8 15.4 - - - -
122C LEU* 3.4 34.1 - - + +
124C THR* 4.6 11.9 - - + -
149C ILE* 4.1 16.8 - - + -
161C PHE* 5.9 2.2 - - + -
162C LEU 3.8 8.4 + - - +
163C LEU* 3.9 24.7 - - + -
164C TRP* 5.3 8.0 + - - +
168C ALA* 4.3 22.1 - - + +
171C LYS* 4.0 31.2 - - + -
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Residues in contact with GLY 62 (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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60C ILE 3.9 0.6 + - - -
61C LEU* 1.3 74.3 - - - +
63C GLN* 1.3 65.0 + - - +
76C ALA* 4.2 8.7 - - - +
77C PHE* 4.3 11.2 - - - -
122C LEU 2.8 10.5 + - - -
123C ASN* 3.5 15.5 - - - -
124C THR* 3.1 26.5 + - - +
168C ALA* 6.0 0.3 - - - +
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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