Contacts of the strand formed by residues 141 - 145 (chain C) in PDB entry 1USK
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 ILE 141 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C ILE* 4.6 4.7 - - + -
133C LEU* 6.1 0.2 - - + -
138C PRO* 3.6 37.7 - - + +
139C GLN 5.6 0.2 - - - +
140C ARG* 1.3 74.6 - - - +
142C ALA* 1.3 65.4 + - - +
143C ILE* 3.6 28.7 - - + -
162C LEU* 4.2 18.8 - - + -
167C ALA* 4.2 24.0 - - + -
168C ASN 3.1 21.0 + - - +
169C VAL* 4.3 5.2 - - + +
170C VAL* 2.8 36.1 + - - +
194C ILE* 4.0 2.7 - - - -
196C PHE* 3.3 19.5 - - + +
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Residues in contact with ALA 142 (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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141C ILE* 1.3 75.4 - - - +
143C ILE* 1.3 66.4 + - - +
144C ILE* 4.8 2.9 - - + -
171C PHE* 3.5 39.0 - - + +
189C LEU* 3.9 8.3 - - + -
194C ILE* 3.8 16.6 - - + -
196C PHE 3.0 6.9 + - - +
197C VAL* 3.3 8.9 - - + +
198C TYR 3.1 23.6 + - - -
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Residues in contact with ILE 143 (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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141C ILE* 3.6 17.9 - - + -
142C ALA* 1.3 80.1 - - - +
144C ILE* 1.3 66.4 + - - +
155C ALA* 3.5 34.3 - - + +
158C VAL* 4.1 4.7 - - + -
159C GLN* 4.5 7.9 - - + +
162C LEU* 4.1 15.3 - - + -
169C VAL* 3.9 22.0 - - + -
171C PHE 3.0 6.0 + - - +
172C PHE* 3.3 27.9 - - + -
173C ASP 3.1 23.9 + - - -
198C TYR* 3.5 24.5 - - + +
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Residues in contact with ILE 144 (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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142C ALA* 4.8 2.7 - - + -
143C ILE* 1.3 83.6 - - - +
145C HIS* 1.3 72.3 + - - +
155C ALA* 4.0 4.9 - - - +
171C PHE* 3.8 19.1 - - + -
173C ASP* 3.3 17.7 - - + +
175C ILE* 4.3 10.8 - - + -
185C LEU* 3.8 43.7 - - + -
189C LEU* 5.5 1.1 - - + -
197C VAL* 4.0 20.9 - - + -
198C TYR 2.9 9.6 + - - +
199C TYR* 3.8 23.6 - - + -
200C GLY* 2.8 22.5 + - - -
209C MET* 4.5 2.5 - - + -
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Residues in contact with HIS 145 (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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144C ILE* 1.3 77.7 - - - +
146C ASP* 1.3 58.2 + - - +
147C LYS* 3.1 32.6 + - + -
152C GLU* 3.6 32.4 + - + +
155C ALA* 3.8 12.8 - - + -
156C ARG* 5.1 1.3 + - - -
172C PHE* 3.2 42.6 - + - -
173C ASP 3.2 10.0 + - - -
174C GLY* 3.4 24.6 + - - -
175C ILE* 3.0 29.3 + - - +
199C TYR* 4.0 7.2 - - - -
200C GLY 3.3 14.4 - - - +
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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