Contacts of the strand formed by residues 218 - 224 (chain C) in PDB entry 3IXK
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 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ARG* 3.5 10.9 - - - -
56C GLY* 2.8 54.3 + - - +
57C LYS 4.0 9.0 - - - +
58C SER* 4.2 17.9 - - - -
59C GLY 5.4 0.9 - - - +
61C GLY 4.6 1.8 - - - +
62C TYR* 3.6 31.2 - - + +
203C CYS 3.3 19.3 - - - +
204C GLY* 3.9 16.2 - - - -
205C ALA 4.0 3.8 - - - +
217C SER* 1.3 79.3 + - - +
219C GLY* 1.3 58.3 + - - +
387C GLU* 5.5 0.2 - - - +
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Residues in contact with GLY 219 (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 ASP* 5.3 0.2 - - - -
54C LEU 3.1 18.2 - - - -
55C ARG* 3.7 9.9 - - - -
62C TYR* 3.3 10.0 - - - -
203C CYS* 2.9 35.5 + - - +
218C VAL* 1.3 76.2 - - - +
220C GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 220 (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 ASP* 3.0 20.7 + - - -
54C LEU* 2.8 37.0 + - - -
55C ARG* 4.2 2.6 - - - +
201C GLN* 3.2 13.5 - - - -
203C CYS* 4.2 11.6 - - - -
219C GLY* 1.3 75.0 - - - -
221C SER* 1.3 59.7 + - - -
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Residues in contact with SER 221 (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 VAL* 3.6 10.4 - - - +
52C ASP* 2.7 24.7 + - - +
53C ASN* 3.5 4.5 - - - -
54C LEU* 3.6 6.8 - - - +
199C SER 3.8 0.9 - - - +
200C LEU* 3.5 3.8 - - - -
201C GLN* 2.9 44.3 + - - +
220C GLY* 1.3 72.0 - - - -
222C MET* 1.3 59.7 + - - +
223C ILE* 3.9 10.5 - - - +
231C LEU* 3.8 24.5 - - - +
390C TYR* 5.7 0.2 - - - -
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Residues in contact with MET 222 (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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50C MET* 3.9 3.6 - - - +
53C ASN* 2.8 35.4 + - - +
54C LEU* 3.7 8.7 - - + +
64C VAL* 5.1 7.0 - - + -
79C VAL* 4.0 23.3 - - - -
135C ILE* 6.0 1.1 - - + -
167C LEU* 4.7 10.3 - - + -
169C LEU* 3.6 34.3 - - + -
185C PHE* 5.3 3.4 - - + -
198C PHE* 4.3 14.6 - - + -
199C SER 3.5 5.8 - - - +
200C LEU* 3.7 19.1 - - + -
221C SER* 1.3 72.8 - - - +
223C ILE* 1.3 62.2 + - - +
224C ILE* 3.5 34.4 + - + +
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Residues in contact with ILE 223 (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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47C PHE* 3.9 31.4 - - + +
50C MET* 4.0 20.9 - - + -
51C VAL* 4.1 17.3 - - + +
198C PHE* 3.1 6.6 - - - +
199C SER* 2.9 46.8 + - - +
221C SER* 4.1 7.4 - - - -
222C MET* 1.3 71.1 - - - +
224C ILE* 1.3 58.7 + - - +
226C GLY 3.3 27.2 - - - +
227C ILE* 4.2 2.5 - - - +
228C ASP* 4.2 4.9 - - + -
231C LEU* 3.7 31.9 - - + -
390C TYR* 3.7 3.6 - - + +
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Residues in contact with ILE 224 (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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47C PHE* 4.5 1.2 - - - -
50C MET* 3.4 24.5 - - - +
53C ASN* 5.1 2.2 - - - +
64C VAL* 6.1 1.3 - - + -
135C ILE* 3.9 30.3 - - + -
138C GLY* 4.2 9.9 - - - -
139C PRO* 3.9 26.9 - - + +
185C PHE* 4.0 10.5 - - + -
188C LEU* 3.7 28.5 - - + -
194C VAL* 4.0 10.2 - - + +
198C PHE* 4.1 4.0 - - + -
222C MET* 3.8 41.1 - - + +
223C ILE* 1.3 72.8 - - - +
225C GLY* 1.3 61.1 + - - +
226C GLY 3.5 0.2 - - - -
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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