Contacts of the helix formed by residues 394 - 401 (chain B) in PDB entry 2AG1
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 ALA 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B GLY* 1.3 72.9 - - - +
395B LEU* 1.3 66.8 + - - +
397B TYR* 2.9 39.2 + - - -
398B LEU* 3.0 20.1 + - + +
421B MSE 3.5 22.9 - - + -
479B GLY 6.0 1.1 - - - +
480B ALA* 3.6 26.0 - - + +
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Residues in contact with LEU 395 (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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393B GLY 3.0 2.4 + - - +
394B ALA* 1.3 78.4 - - - +
396B THR* 1.3 63.0 + - - +
398B LEU* 3.3 6.9 + - + +
399B TRP* 3.0 37.3 + - + +
475B ASN* 3.9 18.4 - - - +
479B GLY* 3.6 26.5 - - - -
480B ALA* 3.4 15.2 - - + +
483B HIS* 3.6 22.7 - - + +
546B LEU* 4.1 5.4 - - + +
548B PRO 4.9 1.3 - - - +
550B PRO* 3.6 27.1 - - + -
553B GLU* 3.2 26.5 - - - +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO* 6.4 0.7 - - - -
376B SER* 4.8 1.2 + - - -
392B ASP 3.5 15.5 - - - +
393B GLY 3.2 13.8 + - - -
395B LEU* 1.3 79.3 - - - +
397B TYR* 1.3 58.7 + - - +
399B TRP* 3.8 4.7 - - - +
400B LEU* 2.9 24.5 + - + +
445B VAL* 3.7 22.2 - - + +
446B THR 4.0 7.9 - - - +
447B GLY* 3.6 12.1 - - - -
473B MSE 3.4 42.9 + - + +
475B ASN* 5.7 2.6 + - - +
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Residues in contact with TYR 397 (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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112A LEU* 5.1 11.4 - - - +
239B TYR* 3.5 31.7 - + - -
282B LEU* 5.8 2.4 - - - +
391B ALA* 3.9 25.1 - - + -
392B ASP 4.0 6.1 - - - +
393B GLY 4.0 0.4 - - - -
394B ALA* 2.9 46.4 + - - -
396B THR* 1.3 77.6 - - - +
398B LEU* 1.3 80.5 + - + +
400B LEU* 3.8 7.7 - - - +
401B SER* 2.9 30.5 + - - -
412B PHE* 5.9 1.1 - - + -
414B CYS* 3.6 17.4 - - - -
415B HIS* 3.4 31.4 - + + +
419B GLY* 6.1 0.5 - - - -
421B MSE 4.5 4.2 - - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 4.3 7.2 - - - +
394B ALA* 3.0 23.8 + - - +
395B LEU* 3.8 7.6 - - + +
397B TYR* 1.3 104.6 - - + +
399B TRP* 1.3 57.1 - - - +
401B SER* 2.8 20.8 + - - +
402B GLU* 3.8 11.6 - - - +
480B ALA* 5.5 4.7 - - + -
550B PRO* 3.8 20.1 - - + +
552B GLU* 3.8 22.4 - - + +
553B GLU* 4.1 31.4 - - + +
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Residues in contact with TRP 399 (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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360B ILE* 3.8 26.7 - - + -
363B LYS 5.9 0.4 - - - -
371B HIS* 3.5 19.5 - + - -
372B PRO* 3.4 38.3 - - + +
373B PHE* 3.9 20.5 - + + -
376B SER* 3.8 15.2 + - - +
395B LEU* 3.0 33.5 + - + +
396B THR* 3.8 4.3 - - - +
398B LEU* 1.3 73.0 - - - +
400B LEU* 1.3 67.3 + - - +
401B SER 3.1 1.8 - - - -
402B GLU* 3.0 22.1 + - + +
403B VAL 4.2 0.9 + - - -
548B PRO* 3.7 24.0 + - + -
549B ILE 3.4 10.1 - - - -
550B PRO* 3.3 48.7 - - + +
551B PRO* 4.0 7.4 - - + -
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Residues in contact with LEU 400 (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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376B SER* 3.5 28.5 - - - +
379B ILE* 4.6 13.7 - - + -
389B VAL* 4.0 20.6 - - + -
391B ALA* 3.8 28.0 - - + -
396B THR 2.9 18.9 + - - +
397B TYR* 3.4 6.2 + - - +
399B TRP* 1.3 75.3 - - - +
401B SER* 1.3 63.5 + - - +
403B VAL* 3.0 32.7 + - + +
404B MSE 3.4 17.2 - - + +
412B PHE* 4.2 7.6 - - + -
445B VAL* 4.1 25.6 - - + -
473B MSE 5.7 0.4 - - + -
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Residues in contact with SER 401 (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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239B TYR* 4.3 12.1 + - - -
256B LEU* 3.5 25.6 - - - +
258B GLN* 2.9 31.6 + - - +
397B TYR 2.9 16.3 + - - -
398B LEU* 2.8 22.5 + - - -
399B TRP 3.1 0.4 - - - -
400B LEU* 1.3 76.1 - - - +
402B GLU* 1.3 60.2 + - - +
403B VAL 3.3 0.7 + - - -
404B MSE 3.4 17.9 + - - -
405B SER* 4.2 3.8 + - - -
412B PHE* 5.3 3.6 - - - -
552B GLU* 4.3 4.2 - - - +
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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