Contacts of the helix formed by residues 488 - 492 (chain A) in PDB entry 2EIT
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 PHE 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A GLY* 2.9 13.6 + - - +
465A HIS* 3.4 51.4 - + + +
466A VAL 3.3 32.8 - - - -
467A GLY* 3.9 5.8 - - - -
487A GLY* 1.3 80.1 - - - -
489A LYS* 1.3 76.0 + - + +
491A SER* 3.0 18.4 + - - -
492A GLY 4.5 2.0 - - - -
494A ASN* 3.6 5.6 - - - -
1520A ACT 4.3 5.4 - - - -
172B VAL* 4.5 5.2 - - + -
254B ARG* 6.1 0.2 - - - +
508B GLU* 3.4 38.4 - - + +
509B MET 3.3 27.6 - - - -
510B LYS* 4.0 12.1 - - + -
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Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASN* 2.9 23.6 + - - +
441A THR 2.7 30.0 + - - -
442A PRO* 3.3 7.4 - - - +
443A TYR 3.2 18.5 + - - +
465A HIS* 3.8 30.0 + - + +
488A PHE* 1.3 80.2 - - + +
490A LEU* 1.3 61.3 + - - +
491A SER 3.1 4.3 + - - -
492A GLY 3.2 16.9 + - - +
254B ARG* 5.2 4.5 + - - +
280B THR* 3.2 30.5 - - - +
281B TRP* 4.0 18.6 - - + +
282B PHE* 3.7 7.3 + - - -
508B GLU* 5.2 2.0 + - - -
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Residues in contact with LEU 490 (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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262A LEU* 3.5 26.7 - - + +
266A LEU* 4.5 0.9 - - + -
289A THR* 2.7 19.7 + - - -
442A PRO* 2.8 34.5 + - + +
443A TYR* 3.5 15.3 - - + -
489A LYS* 1.3 76.5 - - - +
491A SER* 1.3 51.9 + - - +
492A GLY 3.1 5.2 - - - -
275B LEU* 3.8 18.2 - - + -
279B GLN 3.9 15.9 - - - +
280B THR* 3.7 7.6 - - - -
281B TRP* 3.6 27.6 - - - +
282B PHE* 3.9 16.2 - - + -
2533B MPD 4.0 26.7 - - + -
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU* 3.8 9.4 - - - +
289A THR* 2.9 23.6 + - - -
290A GLY 2.6 27.2 + - - +
443A TYR* 3.5 6.7 - - - +
444A GLY 2.8 24.2 + - - -
445A LEU* 3.2 21.8 + - - +
487A GLY* 4.2 6.0 + - - -
488A PHE 3.0 17.2 + - - -
490A LEU* 1.3 74.5 - - - +
492A GLY* 1.3 56.1 + - - +
1518A NAD 4.2 3.3 + - - -
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Residues in contact with GLY 492 (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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287A VAL 3.2 12.6 - - - -
288A GLU* 4.7 0.2 - - - -
289A THR* 3.1 10.8 + - - -
487A GLY 4.3 5.9 - - - +
488A PHE* 4.1 2.2 + - - -
489A LYS 3.2 13.3 + - - +
490A LEU 3.1 3.4 - - - -
491A SER* 1.3 81.3 - - - +
493A THR* 1.3 63.0 + - - -
494A ASN* 3.4 4.4 + - - +
254B ARG* 5.6 4.0 + - - -
282B PHE* 3.6 21.2 + - - +
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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