Contacts of the strand formed by residues 163 - 170 (chain C) in PDB entry 4GUN
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 LEU 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS* 2.8 32.2 + - - -
148B ASP* 5.5 2.2 - - - +
138C VAL* 4.0 22.2 - - + -
139C LYS 3.4 12.6 - - - +
140C ASN* 3.8 26.9 - - + +
150C VAL* 5.9 4.9 - - + -
158C ILE* 3.5 29.8 - - + +
160C ALA* 3.2 19.1 + - + +
161C PRO 4.2 0.4 - - - +
162C HIS* 1.3 96.3 - - + +
164C VAL* 1.4 59.7 + - - +
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Residues in contact with VAL 164 (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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61A LYS* 4.9 1.3 - - - +
138C VAL* 3.3 5.1 - - - -
139C LYS* 2.8 52.6 + - + +
141C LYS* 3.8 39.0 - - + +
158C ILE* 4.6 0.4 - - - -
163C LEU* 1.4 76.8 - - - +
165C PRO* 1.4 79.5 - - + +
166C ILE* 3.4 4.7 + - + +
203C ARG* 3.9 24.2 - - + +
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Residues in contact with PRO 165 (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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61A LYS* 5.0 6.3 - - + +
78C THR* 6.3 0.2 - - + -
82C LEU* 3.9 37.4 - - + +
136C PHE* 4.1 18.4 - - + -
137C ILE 3.9 4.9 - - - +
138C VAL* 4.3 5.2 - - + -
158C ILE* 4.1 23.3 - - + +
163C LEU 4.1 5.8 - - - +
164C VAL* 1.4 89.2 - - + +
166C ILE* 1.3 63.2 + - - +
167C ILE 5.3 2.0 - - - +
203C ARG* 3.5 20.5 + - - +
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Residues in contact with ILE 166 (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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104C LEU* 3.9 19.3 - - + -
137C ILE* 2.7 27.6 + - + +
138C VAL 4.0 2.5 - - - -
139C LYS* 3.8 24.7 - - + +
147C LEU* 4.3 6.5 - - + -
164C VAL* 3.5 21.5 - - + +
165C PRO* 1.3 77.6 - - - +
167C ILE* 1.4 66.5 + - + +
197C TRP* 5.3 1.1 - - + -
200C ALA* 3.6 28.5 - - + +
203C ARG* 3.0 30.3 + - + +
204C TYR* 3.7 33.2 - - + +
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Residues in contact with ILE 167 (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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86C ASN* 3.6 21.1 - - + +
136C PHE* 3.2 10.0 - - - +
137C ILE* 3.0 41.2 + - + +
165C PRO* 5.2 1.1 - - - -
166C ILE* 1.4 88.2 - - + +
168C ALA* 1.4 61.4 + - - +
169C ILE* 3.8 31.6 - - + -
192C TRP* 4.3 12.6 - - + -
195C ILE* 3.7 24.0 - - + -
196C ASN 4.2 2.2 - - - +
197C TRP* 4.0 24.5 - - + -
200C ALA* 3.6 16.6 - - + -
203C ARG* 4.8 0.4 - - - -
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Residues in contact with ALA 168 (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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79C ASN 4.4 0.7 - - - +
82C LEU* 4.0 21.5 - - + -
83C PHE* 3.3 12.0 - - - +
86C ASN* 2.9 32.6 + - - +
134C TRP* 4.1 14.1 - - + -
135C ALA 3.6 4.9 - - - -
136C PHE* 3.6 26.2 - - + -
165C PRO* 5.7 0.2 - - + -
167C ILE* 1.4 73.0 - - - +
169C ILE* 1.3 62.2 + - - +
203C ARG* 4.6 0.4 - - - +
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Residues in contact with ILE 169 (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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83C PHE* 4.0 1.8 - - - -
122C THR* 4.8 4.7 - - + -
126C LEU* 3.8 35.7 - - + +
134C TRP* 3.4 8.6 - - - -
135C ALA 2.9 34.6 + - - +
167C ILE* 3.8 18.6 - - + -
168C ALA* 1.3 73.7 - - - +
170C ASP* 1.3 70.3 + - - +
171C ALA 3.5 0.3 + - - -
187C TYR* 4.7 0.4 - - + +
188C PHE* 4.5 5.2 - - + -
191C ILE* 4.0 32.3 - - + -
192C TRP* 4.2 13.7 - - + -
195C ILE* 3.4 33.2 - - + -
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Residues in contact with ASP 170 (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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32C HIS* 2.9 5.9 + - - -
80C HIS* 3.2 3.6 + - - -
83C PHE* 3.4 26.0 - - + -
134C TRP* 3.5 28.2 - - + -
169C ILE* 1.3 71.5 - - - +
171C ALA* 1.3 59.6 + - - +
172C TRP* 3.0 30.5 + - - +
175C ALA* 3.9 11.0 - - + +
187C TYR* 2.9 30.1 + - - -
301C MN 2.0 35.0 + - - -
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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