Contacts of the helix formed by residues 398 - 403 (chain f) in PDB entry 5T0J
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 TRP 398 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320f LEU* 5.0 2.8 - - + +
353f MET* 3.6 28.0 - - + +
361f LEU* 3.5 51.3 - - + +
365f MET* 4.0 15.5 - - + -
394f THR 4.4 10.8 - - - -
395f TYR* 3.3 12.0 + - + +
397f ARG* 1.3 83.0 - - + +
399f LEU* 1.3 65.9 + - - +
401f LEU* 3.1 41.2 + - + +
402f GLY 4.0 1.4 + - - -
672f VAL* 5.8 1.1 - - + -
676f GLU* 3.2 35.3 + - + -
690f ALA* 3.1 44.3 - - + +
693f VAL* 3.7 17.9 - - + -
694f VAL* 6.3 0.7 - - + -
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Residues in contact with LEU 399 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360f ALA 5.4 0.7 - - - +
364f GLY* 6.1 3.6 - - - -
379f ILE* 3.8 28.2 - - + +
383f ILE* 3.6 33.0 - - + -
390f GLU* 4.8 2.2 - - - +
395f TYR* 3.5 40.8 + - + +
396f ALA* 4.7 1.3 - - - +
398f TRP* 1.3 78.6 - - - +
400f PRO* 1.3 68.1 - - + +
402f GLY* 3.0 16.3 + - - -
403f LEU* 4.2 3.1 + - - +
414f ILE* 3.8 17.9 - - + +
418f LEU* 3.6 26.7 - - + -
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Residues in contact with PRO 400 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396f ALA 3.2 16.6 - - - +
397f ARG 3.3 8.7 - - - +
399f LEU* 1.3 92.3 - - + +
401f LEU* 1.3 57.6 + - - +
402f GLY 3.1 2.2 + - - -
403f LEU* 3.4 12.5 + - + +
404f GLY* 3.5 3.3 + - - -
405f LEU* 4.5 0.3 - - - +
414f ILE* 5.7 1.1 - - + -
436f VAL 4.0 0.9 - - - +
437f ASP* 3.3 38.4 - - - +
440f ALA* 2.9 50.8 - - + +
441f TYR* 3.5 17.0 - - + -
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Residues in contact with LEU 401 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361f LEU* 5.5 3.1 - - + -
364f GLY 4.4 4.2 - - - +
365f MET* 5.0 8.7 - - + -
397f ARG 3.3 21.3 - - - +
398f TRP* 3.1 37.1 + - + +
400f PRO* 1.3 77.4 - - - +
402f GLY* 1.3 55.8 + - - +
403f LEU 3.4 0.7 - - - -
405f LEU* 3.3 44.8 - - + +
436f VAL* 4.8 1.3 - - + -
440f ALA* 4.5 12.1 - - + -
671f LEU* 4.8 4.3 - - + +
672f VAL* 3.8 31.6 - - + -
675f ASP* 3.2 31.9 - - + +
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Residues in contact with GLY 402 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364f GLY* 3.4 33.4 - - - +
367f ALA* 5.4 0.7 - - - +
370f SER 4.8 8.3 - - - +
371f CYS 5.8 0.2 + - - -
379f ILE* 4.5 14.4 - - - +
398f TRP 4.0 2.0 + - - -
399f LEU* 3.0 13.2 + - - -
401f LEU* 1.3 78.0 - - - +
403f LEU* 1.3 59.0 + - - +
405f LEU* 5.1 2.0 - - - -
406f ASN* 5.4 5.6 - - - +
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Residues in contact with LEU 403 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376f THR* 4.6 19.7 - - + +
380f LEU* 5.0 8.1 - - + -
399f LEU 5.0 2.7 - - - +
400f PRO* 3.4 7.9 + - + +
401f LEU 3.4 1.0 - - - -
402f GLY* 1.3 81.9 - - - +
404f GLY* 1.3 68.8 + - - +
405f LEU 3.2 1.8 + - - -
406f ASN* 3.4 3.5 + - - +
407f HIS* 3.0 25.9 + - + +
410f LYS* 3.8 30.5 - - + -
412f GLU* 3.9 18.2 - - + +
414f ILE* 3.8 35.4 - - + +
441f TYR* 3.9 15.3 - - + +
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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