Contacts of the helix formed by residues 315 - 320 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ARG* 3.6 21.2 - - - +
314A LEU* 1.3 88.5 - - + +
316A ILE* 1.3 57.6 + - - +
317A THR* 3.0 22.0 - - + +
318A CYS* 2.9 36.5 + - + +
323A PRO* 4.7 18.2 - - + -
123D GLU* 3.2 20.4 - - - +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 4.0 18.2 - - - +
186A GLU 4.3 14.1 - - - +
187A ASP 5.9 0.2 - - - -
188A LEU* 4.1 30.3 - - + -
313A ARG* 3.9 11.2 - - - +
314A LEU 4.4 1.8 - - - +
315A PRO* 1.3 72.3 - - - +
317A THR* 1.3 61.3 + - - +
318A CYS 3.0 1.3 + - - -
319A LEU* 3.1 26.1 + - + +
320A THR* 4.7 0.7 + - - -
81D PHE* 3.9 26.8 - - + -
89D MET* 3.9 15.4 - - + +
119D LEU* 5.1 10.3 - - + -
122D ASP* 5.7 4.7 - - + +
123D GLU* 3.1 19.7 + - + +
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PRO* 3.6 19.7 - - + +
316A ILE* 1.3 73.8 - - - +
318A CYS* 1.3 57.1 + - - +
319A LEU 3.0 5.8 - - - -
320A THR* 2.9 10.2 + - - -
321A ILE* 2.9 44.7 + - - +
322A PRO 5.7 0.2 + - - -
323A PRO* 5.4 4.0 - - - +
56D VAL* 6.1 0.7 - - - -
89D MET* 3.5 47.8 - - + +
90D THR* 3.8 12.3 - - + -
123D GLU* 4.7 6.3 - - + -
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Residues in contact with CYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.2 12.0 - - - +
145A ARG* 2.8 22.1 + - - +
152A GLU* 3.6 18.2 - - - +
156A TYR* 3.8 15.7 - - - -
188A LEU* 3.4 26.2 - - - -
314A LEU* 3.8 15.3 - - + -
315A PRO* 2.9 28.1 + - + +
317A THR* 1.3 77.9 + - - +
319A LEU* 1.3 62.0 + - - +
320A THR 3.1 2.5 - - - -
321A ILE 3.5 10.8 - - - -
323A PRO* 4.5 7.0 - - + -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 4.0 22.7 - - + +
141A LEU* 3.9 20.1 - - + +
144A ARG* 2.8 30.7 - - - +
145A ARG* 4.4 1.8 - - - +
184A LEU* 4.4 14.1 - - + -
188A LEU* 4.3 25.6 - - + -
316A ILE* 3.1 29.0 + - + +
317A THR 3.0 2.0 - - - -
318A CYS* 1.3 81.8 - - - +
320A THR* 1.3 62.1 + - - +
79D TYR* 3.9 43.1 + - + +
81D PHE* 4.2 7.9 - - + -
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 2.9 40.2 + - - +
145A ARG* 3.6 13.0 - - - +
316A ILE 5.0 1.0 + - - -
317A THR* 2.9 6.7 + - - -
318A CYS 3.1 0.6 - - - -
319A LEU* 1.3 84.6 - - - +
321A ILE* 1.3 62.7 + - + +
23D ARG* 4.6 8.8 + - - +
48D LEU* 4.4 15.0 - - + -
53D LEU* 5.4 2.2 - - + -
56D VAL* 4.0 36.3 - - + -
81D PHE* 4.7 1.9 - - - -
86D LEU* 4.0 17.6 - - + +
89D MET* 5.5 0.3 - - - -
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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