Contacts of the helix formed by residues 298 - 305 (chain B) in PDB entry 4PEI
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 SER 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B LEU 5.0 0.2 - - - -
296B SER 3.7 2.4 + - - -
297B TYR* 1.3 71.5 - - - +
299B ILE* 1.3 59.3 + - - +
300B SER* 3.6 4.0 + - - -
301B GLU* 3.1 32.9 + - - +
302B LEU* 2.9 32.8 + - - +
163C GLN* 3.6 17.4 + - - -
298C SER* 5.7 0.9 + - - -
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Residues in contact with ILE 299 (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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160B TYR* 4.8 8.3 - - + -
163B GLN* 3.5 39.4 - - + +
164B MET* 3.6 24.0 - - - -
282B THR* 4.0 15.9 - - + -
285B ALA* 3.5 32.5 - - + -
286B PHE* 4.4 12.1 - - + -
293B PRO* 5.2 0.9 - - + -
295B LEU* 4.0 24.4 - - + +
297B TYR 3.7 1.0 + - - +
298B SER* 1.3 69.8 + - - +
300B SER* 1.3 67.8 + - - +
302B LEU* 3.3 5.9 + - + +
303B LEU* 2.9 26.9 + - + +
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Residues in contact with SER 300 (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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163B GLN* 4.3 19.3 - - - +
298B SER* 3.3 1.9 + - - -
299B ILE* 1.3 81.1 - - - +
301B GLU* 1.3 55.9 + - - +
303B LEU* 3.2 8.2 + - - +
304B SER* 2.8 27.9 + - - -
162C ILE* 4.7 9.5 - - - +
163C GLN* 3.4 38.9 + - - +
300C SER* 5.1 2.2 - - - -
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Residues in contact with GLU 301 (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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297B TYR* 6.5 0.2 - - + -
298B SER* 3.1 29.5 + - - +
300B SER* 1.3 75.5 - - - +
302B LEU* 1.3 72.6 + - + +
304B SER* 2.3 34.0 + - - -
305B LYS* 2.7 33.7 + - - +
138C GLU* 4.6 4.0 - - - +
139C LYS* 2.5 42.8 + - - -
159C ASN* 3.5 28.2 + - - +
163C GLN* 4.7 1.9 - - - +
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Residues in contact with LEU 302 (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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281B MET* 3.7 25.4 - - - +
282B THR* 4.2 14.1 - - + -
284B PRO* 4.1 19.5 - - + -
285B ALA* 3.9 33.9 - - + +
297B TYR* 3.9 26.5 - - + -
298B SER 2.9 23.1 + - - +
299B ILE* 3.7 6.7 - - + +
301B GLU* 1.3 80.2 - - + +
303B LEU* 1.3 62.6 + - - +
305B LYS* 3.3 41.4 + - + +
348B TYR* 5.4 1.6 - - - +
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Residues in contact with LEU 303 (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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163B GLN 3.4 26.2 - - - +
164B MET* 4.4 3.1 - - - -
167B ASN* 4.0 24.0 + - - +
278B ASN* 3.6 39.9 - - + +
281B MET* 4.2 9.2 - - + -
282B THR* 3.4 24.7 - - + -
299B ILE* 2.9 27.7 + - + +
300B SER* 3.9 5.6 - - - +
302B LEU* 1.3 70.2 - - - +
304B SER* 1.3 63.2 + - - +
305B LYS 2.9 7.0 + - - -
306B ARG* 3.1 23.2 + - - +
216C VAL* 5.5 0.5 - - - +
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Residues in contact with SER 304 (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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300B SER* 2.8 13.4 + - - -
301B GLU* 2.3 39.3 + - - -
303B LEU* 1.3 77.4 - - - +
305B LYS* 1.3 62.0 + - - +
306B ARG 3.4 5.0 + - - +
138C GLU* 4.9 0.2 + - - -
159C ASN* 3.2 19.1 + - - -
162C ILE* 3.9 19.3 - - - -
212C PRO* 5.2 6.9 - - - +
215C LYS* 5.0 2.1 + - - -
216C VAL* 3.7 26.0 - - - +
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Residues in contact with LYS 305 (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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281B MET* 3.3 18.2 - - + +
301B GLU* 2.7 36.9 + - - +
302B LEU* 3.4 39.6 - - + +
303B LEU 2.9 2.0 - - - -
304B SER* 1.3 79.6 - - - +
306B ARG* 1.3 67.0 + - - +
307B THR* 3.5 10.1 + - - +
310B LEU* 4.4 5.2 - - - +
348B TYR* 5.5 3.6 + - - -
353B ILE* 6.1 3.1 - - + -
138C GLU* 6.1 0.9 - - - +
139C LYS* 4.5 4.0 - - - +
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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