Contacts of the helix formed by residues 321 - 325 (chain D) in PDB entry 2IB8
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 GLU 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ILE* 3.7 33.5 - - - +
320D VAL* 1.3 78.1 - - - +
322D PRO* 1.4 76.2 - - + +
323D ILE* 3.2 11.0 - - + -
324D ASP* 2.7 50.2 + - - +
325D PHE 3.7 0.3 + - - -
417D GLY* 4.0 0.2 - - - -
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Residues in contact with PRO 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ARG* 4.7 1.6 - - - +
109C LEU* 4.3 10.1 - - + -
115C ILE* 4.8 4.9 - - + -
186D ASP* 3.4 29.9 - - - +
188D TYR* 3.7 27.8 - - + -
189D ASN* 4.4 3.4 - - - +
196D CYS* 4.9 0.5 - - - -
320D VAL 3.3 2.9 - - - +
321D GLU* 1.4 100.1 - - + +
323D ILE* 1.3 60.2 + - - +
324D ASP 3.3 0.5 + - - -
325D PHE* 3.5 22.7 + - - +
416D GLY 3.5 25.7 + - - +
417D GLY* 3.8 2.5 + - - -
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Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ASN* 3.7 30.4 - - - +
191D ILE* 4.8 9.6 - - + -
195D SER 5.5 0.4 - - - +
196D CYS* 3.6 45.3 - - + +
199D ASN* 3.8 32.3 - - + +
200D THR* 4.7 0.9 + - - -
203D LYS* 6.0 0.2 - - - -
321D GLU* 4.5 11.0 - - + -
322D PRO* 1.3 79.5 - - - +
324D ASP* 1.3 80.4 + - - +
325D PHE 3.3 4.0 + - - -
326D PRO* 3.7 6.8 - - - +
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Residues in contact with ASP 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASN* 3.5 21.0 - - - +
200D THR* 4.2 8.3 + - - +
203D LYS* 4.2 16.6 + - - +
320D VAL* 3.4 10.2 - - + +
321D GLU* 2.7 30.9 + - + +
323D ILE* 1.3 84.5 - - - +
325D PHE* 1.3 62.6 + - - +
326D PRO* 3.0 6.7 - - - -
327D ILE* 2.9 42.5 + - + +
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Residues in contact with PHE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D MET* 3.5 40.6 - - + -
196D CYS* 3.5 27.1 - - + -
197D ALA* 4.4 2.0 - - + -
321D GLU 3.7 1.2 + - - -
322D PRO 3.5 13.7 + - - +
323D ILE 3.3 3.5 - - - -
324D ASP* 1.3 75.4 - - - +
326D PRO* 1.4 82.5 - - + +
327D ILE 3.2 0.7 + - - -
328D ALA* 3.3 13.9 + - - +
329D PRO* 3.4 0.5 - - - +
356D PHE* 4.0 25.8 - + - -
359D VAL* 4.5 0.9 - - + -
413D CYS* 3.3 42.0 - - + +
414D ASN 3.8 15.5 - - - +
415D GLY* 5.5 2.2 - - - -
416D GLY 5.6 0.4 - - - -
417D GLY* 3.7 26.9 - - - +
418D GLY 4.6 0.7 - - - +
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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