Contacts of the helix formed by residues 395 - 404 (chain B) in PDB entry 5DQE
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B LEU* 3.3 3.2 - - - +
394B PRO* 1.3 93.2 - - + +
396B ARG* 1.3 61.1 + - - +
397B TYR* 3.3 38.7 - - + +
398B MET* 3.1 33.7 + - + +
399B MET* 3.2 17.3 + - - +
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Residues in contact with ARG 396 (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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303B TRP* 5.3 2.8 - - - -
395B GLU* 1.3 72.1 + - - +
397B TYR* 1.3 62.6 + - - +
398B MET 3.1 0.2 + - - -
399B MET* 3.1 14.5 + - - +
400B ASN* 2.8 49.0 + - - +
429B GLU* 4.6 5.3 + - - -
430B VAL* 2.7 55.2 + - + -
431B SER* 4.0 1.5 - - - +
432B THR* 3.5 46.2 - - - +
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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
----------------------------------------------------------
395B GLU* 3.3 36.7 - - + +
396B ARG* 1.3 79.1 - - - +
398B MET* 1.3 90.2 + - + +
400B ASN* 3.5 10.5 + - - +
401B SER* 2.9 35.9 + - - -
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Residues in contact with MET 398 (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 LEU* 4.0 14.8 - - + -
394B PRO* 4.0 27.1 - - + -
395B GLU* 3.1 21.9 + - + +
397B TYR* 1.3 114.9 - - + +
399B MET* 1.3 60.2 + - - +
401B SER* 3.2 7.6 + - - -
402B VAL* 3.0 33.2 + - + +
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Residues in contact with MET 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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306B LEU* 4.8 7.6 - - + -
390B LEU* 3.3 35.6 - - + +
391B ARG* 3.8 12.8 - - - +
393B LEU* 3.5 34.7 - - + +
395B GLU 3.7 10.5 - - - +
396B ARG* 3.1 13.4 + - - +
398B MET* 1.3 76.1 - - - +
400B ASN* 1.3 60.2 + - - +
402B VAL* 3.4 2.8 + - - +
403B LEU* 3.0 33.1 + - - +
430B VAL* 3.8 38.8 - - + -
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Residues in contact with ASN 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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396B ARG* 2.8 47.3 + - - +
397B TYR* 3.7 8.4 - - - +
399B MET* 1.3 74.5 - - - +
401B SER* 1.3 64.3 + - - +
403B LEU* 3.2 5.6 + - - +
404B GLU* 3.0 31.0 + - + +
428B PHE 5.0 1.2 - - - +
429B GLU* 3.5 27.2 + - + +
430B VAL* 2.8 33.3 + - - +
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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
----------------------------------------------------------
397B TYR* 2.9 23.8 + - - -
398B MET* 3.2 10.1 + - - -
400B ASN* 1.3 74.2 - - - +
402B VAL* 1.3 63.5 + - - +
404B GLU* 3.3 25.6 + - - +
405B ASN* 3.5 14.9 + - - -
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Residues in contact with VAL 402 (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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350B PHE* 5.9 0.2 - - - -
386B PHE* 3.9 29.4 - - + -
390B LEU* 4.1 9.6 - - + -
393B LEU* 4.0 16.4 - - + -
398B MET* 3.0 18.8 + - + +
399B MET 3.7 6.5 - - - +
400B ASN 3.3 0.2 - - - -
401B SER* 1.3 76.3 - - - +
403B LEU* 1.3 63.9 + - - +
405B ASN* 3.2 17.8 + - - +
406B PHE* 3.4 18.1 - - + -
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Residues in contact with LEU 403 (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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304B ALA* 5.9 1.8 - - + -
386B PHE* 4.0 28.7 - - + -
390B LEU* 4.0 13.2 - - + -
399B MET 3.0 18.3 + - - +
400B ASN* 3.2 4.5 + - - +
402B VAL* 1.3 71.9 - - - +
404B GLU* 1.3 65.1 + - - +
405B ASN 3.0 3.4 + - - -
406B PHE* 3.1 30.3 + - + +
428B PHE* 3.5 38.6 + - + +
429B GLU* 4.0 17.3 - - - +
430B VAL* 3.5 32.1 - - + +
502B 5E4 3.8 6.2 - - - -
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Residues in contact with GLU 404 (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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277B LYS* 3.5 36.3 + - - +
400B ASN* 3.0 16.7 + - - +
401B SER* 3.5 23.9 + - - +
402B VAL 3.1 1.0 - - - -
403B LEU* 1.3 77.9 - - - +
405B ASN* 1.3 65.0 + - - +
406B PHE 3.4 0.6 + - - -
502B 5E4 3.6 25.4 - - + -
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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