Contacts of the helix formed by residues 315 - 320 (chain B) in PDB entry 2V5Q
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 PRO 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 5.9 0.4 - - - +
188B LEU* 3.7 1.2 - - - +
313B ARG* 4.6 11.7 - - - +
314B LEU* 1.3 92.9 - - + +
316B ILE* 1.3 59.3 + - - +
317B THR* 3.1 18.8 - - - +
318B CYS* 3.0 37.6 + - + +
323B PRO* 5.4 12.8 - - + -
122C ASP* 5.7 0.7 - - - +
123C GLU* 3.3 20.9 - - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ARG* 3.7 35.2 - - - +
186B GLU 5.5 2.5 - - - +
188B LEU* 4.1 16.8 - - + +
314B LEU 4.0 0.2 + - - -
315B PRO* 1.3 71.9 - - - +
317B THR* 1.3 64.4 + - - +
318B CYS 3.1 1.1 + - - -
319B LEU* 3.5 29.6 + - + +
320B THR* 4.9 0.7 + - - -
81C PHE* 4.2 14.2 - - + -
89C MET* 3.8 28.3 - - + +
119C LEU* 4.5 19.5 - - + +
122C ASP* 4.3 16.7 + - - +
123C GLU* 3.9 15.8 + - + +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PRO* 3.6 16.5 - - - +
316B ILE* 1.3 73.9 - - - +
318B CYS* 1.3 56.8 + - - +
319B LEU 3.0 5.8 - - - -
320B THR* 2.8 21.0 + - - -
321B ILE* 2.9 38.4 + - + +
322B PRO 5.3 0.2 + - - -
323B PRO* 5.1 8.0 - - - +
89C MET* 3.5 41.1 - - + +
90C THR* 4.9 1.1 - - + -
123C GLU* 3.6 24.2 + - + +
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Residues in contact with CYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.9 9.1 - - - +
145B ARG* 2.8 27.7 + - - +
152B GLU* 3.6 19.1 - - - +
156B TYR* 4.2 8.1 - - - -
188B LEU* 3.9 14.4 - - - -
314B LEU* 3.9 29.4 - - + -
315B PRO* 3.0 26.9 + - + +
317B THR* 1.3 79.8 + - - +
319B LEU* 1.3 69.2 + - - +
320B THR 3.2 0.2 - - - -
321B ILE 3.6 8.7 - - - -
323B PRO* 5.9 1.6 - - + -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 4.2 8.7 - - - +
141B LEU* 3.9 26.8 - - + -
144B ARG* 2.9 31.9 - - - +
145B ARG* 4.2 3.5 - - - +
184B LEU* 4.1 16.8 - - + -
188B LEU* 4.2 10.8 - - + -
316B ILE* 3.6 35.9 - - + +
317B THR 2.9 0.8 + - - -
318B CYS* 1.3 83.7 - - - +
320B THR* 1.3 63.2 + - - +
79C TYR* 3.9 43.7 + - + +
81C PHE* 4.0 11.9 - - + -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ARG* 3.0 34.2 + - - +
145B ARG* 3.5 10.4 - - - +
316B ILE 5.0 0.5 + - - -
317B THR 2.8 4.6 + - - -
318B CYS 3.2 0.2 - - - -
319B LEU* 1.3 85.9 - - - +
321B ILE* 1.3 66.3 + - - +
23C ARG* 3.9 18.2 + - - +
48C LEU* 4.6 12.6 - - + -
53C LEU* 6.0 0.2 - - + -
56C VAL* 4.1 26.7 - - + -
81C PHE* 4.5 3.3 - - - -
86C LEU* 4.2 16.4 - - + +
89C MET* 4.3 11.8 - - - +
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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
------------------------------------------------------------
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