Contacts of the strand formed by residues 246 - 253 (chain C) in PDB entry 5IWI
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 ARG 246 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C GLY* 4.4 3.2 + - - -
223C LEU* 3.8 22.9 - - + +
245C SER* 1.3 72.9 - - - +
247C ALA* 1.3 61.6 + - - +
248C VAL* 5.5 7.1 - - + +
261C VAL* 3.3 3.6 - - - +
262C THR* 3.0 40.8 + - - +
263C GLU* 2.8 56.6 + - + +
485C ARG 5.3 2.4 + - - -
487C GLU* 2.9 44.9 + - - +
489C GLN* 5.8 1.0 - - - +
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Residues in contact with ALA 247 (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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245C SER* 3.6 6.1 + - - +
246C ARG* 1.3 76.5 - - - +
248C VAL* 1.3 70.1 + - - +
259C ILE* 4.2 5.2 - - + -
260C VAL 3.2 5.2 - - - +
261C VAL* 3.9 21.1 - - + -
318C LEU* 4.1 25.2 - - + +
322C TYR* 4.0 17.9 + - - +
327C LEU* 5.1 0.2 - - + -
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Residues in contact with VAL 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ARG* 5.5 8.3 - - + +
247C ALA* 1.3 79.6 - - - +
249C ILE* 1.3 69.5 + - - +
250C GLU* 4.6 13.2 - - + +
258C ARG 3.8 0.3 - - - +
259C ILE* 3.3 5.5 - - - +
260C VAL* 2.8 52.6 + - + +
262C THR* 6.2 1.8 - - + -
318C LEU* 5.7 1.1 - - - -
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Residues in contact with ILE 249 (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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248C VAL* 1.3 78.4 - - - +
250C GLU* 1.3 64.0 + - - +
257C GLN* 3.7 25.6 - - - +
258C ARG 3.4 6.3 - - - +
259C ILE* 4.1 12.1 - - + -
314C ALA* 3.7 22.2 - - + +
315C SER* 3.2 44.4 - - - +
318C LEU* 4.4 15.5 - - + -
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Residues in contact with GLU 250 (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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248C VAL* 4.6 11.0 - - + +
249C ILE* 1.3 77.8 - - - +
251C GLU* 1.3 63.7 + - + +
257C GLN* 3.3 8.0 - - - +
258C ARG* 2.8 77.4 + - + +
260C VAL* 3.5 15.3 - - + +
303C ARG* 3.5 14.7 + - - -
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Residues in contact with GLU 251 (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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250C GLU* 1.3 86.3 - - + +
252C ARG* 1.3 60.3 + - - +
253C GLY 4.6 3.8 + - - +
256C ARG 3.4 6.3 - - - -
257C GLN* 4.3 3.9 - - - +
258C ARG* 4.1 7.1 + - - -
503C GOL 3.5 40.0 + - - +
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Residues in contact with ARG 252 (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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251C GLU* 1.3 74.5 - - - +
253C GLY* 1.3 59.4 + - - +
256C ARG* 2.8 53.2 + - + +
257C GLN 2.9 21.0 + - - +
258C ARG* 3.5 31.0 + - + +
290C THR* 3.5 16.8 + - - +
307C ASP* 3.4 36.6 + - - +
308C VAL 2.9 24.5 + - - -
309C ARG* 4.8 1.2 - - - +
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Residues in contact with GLY 253 (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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251C GLU* 3.7 6.5 - - - +
252C ARG* 1.3 82.7 - - - +
254C GLY* 1.3 64.2 + - - -
255C GLY 3.2 3.1 - - - -
256C ARG* 3.1 26.1 + - - +
503C GOL 5.1 0.8 + - - -
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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