Contacts of the strand formed by residues 301 - 306 (chain C) in PDB entry 3VI4
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 ASP 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C PHE* 4.2 4.3 - - - -
290C ALA 3.9 0.2 - - - +
291C ALA* 3.4 6.6 - - - +
292C THR 2.6 34.7 + - - +
293C ASP* 3.0 1.4 - - - +
294C VAL* 2.9 37.6 + - + +
295C ASN* 3.3 1.7 - - - +
299C LEU 3.1 2.3 - - - +
300C ASP* 1.3 73.6 - - - +
302C LEU* 1.3 62.9 + - - +
303C LEU* 4.1 2.5 - - - +
326C VAL* 5.0 1.1 - - + -
327C TYR 3.6 12.3 - - - +
328C LEU* 3.3 18.3 - - + +
329C GLN 2.8 23.3 + - - +
2002C CA 2.3 30.6 - - - -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 4.4 10.7 - - + -
249C VAL* 3.9 30.5 - - + -
262C VAL* 4.7 4.0 - - + -
264C ILE* 4.0 9.9 - - + -
276C PHE* 3.4 44.9 - - + -
290C ALA 3.7 8.5 - - - +
301C ASP* 1.3 73.3 - - - +
303C LEU* 1.3 79.5 + - - +
304C VAL* 3.9 17.9 - - + -
326C VAL* 3.2 6.6 - - - +
327C TYR* 2.8 51.8 + - + +
334C ILE* 5.3 1.6 - - + -
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C VAL* 3.4 5.2 - - - -
290C ALA* 2.7 52.7 + - + +
292C THR* 3.8 28.5 - - + -
294C VAL* 4.4 12.6 - - + -
301C ASP 4.1 4.9 - - - +
302C LEU* 1.3 83.1 - - - +
304C VAL* 1.3 64.2 - - - +
324C VAL* 4.2 11.7 - - + -
325C TYR 3.4 3.6 - - - +
326C VAL* 3.9 13.9 - - + -
355C LEU* 3.5 10.0 - - + +
369C VAL* 3.9 21.8 - - + -
394C LEU* 3.8 26.9 - - + -
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Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C VAL* 3.5 35.7 - - + -
276C PHE* 5.5 0.2 - - + -
285C PHE* 3.7 21.8 - - + -
286C GLY 3.6 9.4 - - - +
288C ALA 3.8 4.5 - - - +
289C VAL* 4.4 1.3 - - + -
302C LEU* 3.9 17.3 - - + -
303C LEU* 1.3 79.7 - - - +
305C GLY* 1.3 74.3 + - - +
323C ARG 3.7 0.2 - - - +
324C VAL* 3.2 8.5 - - - +
325C TYR* 2.8 37.3 + - + +
327C TYR* 3.9 19.5 - - + -
355C LEU* 4.1 4.0 - - - -
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Residues in contact with GLY 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C TYR 4.0 0.9 - - - -
285C PHE* 3.3 0.9 - - - -
286C GLY 2.9 26.0 + - - -
287C TYR 4.5 1.8 - - - -
288C ALA* 2.8 20.4 + - - -
304C VAL* 1.3 75.2 - - - +
306C ALA* 1.3 63.9 + - - +
307C PRO* 4.0 4.0 - - - -
323C ARG 3.9 2.5 - - - -
324C VAL* 4.7 1.3 - - - -
352C GLY* 3.4 22.9 - - - -
355C LEU* 3.9 4.3 - - - +
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Residues in contact with ALA 306 (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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283C SER* 4.4 10.5 - - - +
284C TYR 3.6 7.0 - - - -
285C PHE* 3.9 15.5 - - + +
305C GLY* 1.3 76.3 - - - +
307C PRO* 1.3 66.8 - - - +
308C LEU 3.0 9.9 + - - -
309C LEU* 3.3 8.7 + - - +
323C ARG* 3.0 32.0 + - + +
325C TYR* 3.7 21.8 - - + +
352C GLY* 4.2 2.0 + - - -
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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