Contacts of the helix formed by residues 488 - 492 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A VAL* 4.4 5.6 - - + -
508A GLU* 3.4 37.9 - - + +
509A MET 3.3 28.3 - - - -
510A LYS* 4.0 12.8 - - + -
444B GLY* 2.9 14.7 + - - +
465B HIS* 3.4 50.9 - + + +
466B VAL 3.4 29.4 - - - -
467B GLY* 3.9 7.0 - - - -
487B GLY* 1.3 79.4 - - - -
489B LYS* 1.3 75.7 + - + +
491B SER* 3.1 17.9 + - - -
492B GLY 4.5 2.0 - - - -
494B ASN* 3.5 7.2 - - - -
2520B ACT 4.4 6.3 - - - -
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ARG* 5.1 6.3 - - - +
280A THR* 3.1 31.4 - - - +
281A TRP* 4.0 19.9 - - + +
282A PHE* 3.6 7.3 + - - -
508A GLU* 5.2 0.2 + - - -
439B ASN* 2.9 23.6 + - - +
441B THR 2.7 28.8 + - - -
442B PRO* 3.4 8.1 - - - +
443B TYR 3.2 18.3 + - - +
465B HIS* 3.7 31.0 + - + +
488B PHE* 1.3 80.3 - - + +
490B LEU* 1.3 61.7 + - - +
491B SER 3.1 4.7 + - - -
492B GLY 3.3 17.3 + - - +
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Residues in contact with LEU 490 (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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275A LEU* 3.8 18.8 - - + -
279A GLN 4.0 13.9 - - - +
280A THR* 3.7 7.2 - - - -
281A TRP* 3.6 27.8 - - - +
282A PHE* 3.9 16.8 - - + -
2535A MPD 3.9 35.7 - - + +
262B LEU* 3.5 26.1 - - + +
266B LEU* 4.5 1.1 - - + -
289B THR* 2.5 21.7 + - - -
442B PRO* 2.8 26.9 + - + +
443B TYR* 3.6 13.5 - - + -
489B LYS* 1.3 76.8 - - - +
491B SER* 1.3 49.6 + - - +
492B GLY 3.2 4.9 - - - -
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Residues in contact with SER 491 (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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288B GLU* 3.7 9.0 - - - +
289B THR* 2.8 27.8 + - - +
290B GLY 2.8 21.5 + - - -
443B TYR* 3.5 4.9 - - - +
444B GLY 2.8 25.0 + - - -
445B LEU* 3.2 24.2 + - - +
487B GLY* 4.2 6.9 + - - -
488B PHE 3.1 15.9 + - - -
489B LYS 3.1 1.4 + - - -
490B LEU* 1.3 74.9 - - - +
492B GLY* 1.3 55.7 + - - +
2518B NAD 4.2 2.3 + - - -
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Residues in contact with GLY 492 (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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254A ARG* 5.6 3.5 + - - -
282A PHE* 3.6 25.8 + - - +
287B VAL 3.0 14.1 - - - -
288B GLU* 4.3 0.4 - - - -
289B THR* 3.7 2.2 - - - -
487B GLY 4.2 6.0 - - - +
488B PHE* 4.2 2.3 + - - -
489B LYS 3.3 14.4 + - - +
490B LEU 3.2 4.0 - - - -
491B SER* 1.3 81.3 - - - +
493B THR* 1.3 62.2 + - - -
494B ASN* 3.4 3.8 + - - +
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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
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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