Contacts of the helix formed by residues 399 - 404 (chain D) in PDB entry 4EJX
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 VAL 399 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.8 17.3 - - + -
73B THR* 4.5 6.3 - - + +
76B LEU* 3.5 31.9 - - + -
336D HIS 5.4 0.2 + - - -
339D ILE* 3.7 30.5 + - + +
341D PRO* 4.1 24.0 - - + -
390D LYS* 3.9 10.2 - - + +
398D ALA* 1.3 73.7 - - - +
400D ASP* 1.3 62.0 + - - +
401D GLU* 3.2 10.1 - - + +
402D ILE* 3.2 14.4 + - + +
403D ARG* 2.9 24.3 + - - +
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Residues in contact with ASP 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 4.4 16.4 + - - +
71B PHE* 4.3 15.3 + - - +
73B THR* 4.2 13.7 + - - +
398D ALA 3.9 0.9 + - - +
399D VAL* 1.3 70.1 - - - +
401D GLU* 1.3 60.5 + - - +
402D ILE 3.2 0.4 - - - -
403D ARG* 2.9 34.4 + - - +
404D GLU* 2.7 45.5 + - + +
405D ARG* 3.1 28.9 + - - +
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Residues in contact with GLU 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B THR* 6.1 0.7 - - + +
341D PRO* 3.4 41.5 - - + +
342D PHE* 6.2 0.6 - - - -
360D PRO* 4.0 9.1 - - - +
361D LEU* 3.4 19.2 + - + -
362D SER* 2.9 36.2 + - - -
365D PHE* 3.7 9.1 - - - -
399D VAL* 3.2 5.8 - - + -
400D ASP* 1.3 77.0 - - - +
402D ILE* 1.3 59.3 + - - +
405D ARG* 3.1 55.4 + - - +
406D LEU 3.3 0.5 + - - -
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Residues in contact with ILE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D HIS* 3.6 30.1 - - + +
339D ILE* 4.3 17.7 - - + -
361D LEU* 4.2 13.9 - - + -
365D PHE* 3.8 22.2 - - + -
398D ALA* 4.1 12.3 - - + -
399D VAL* 3.4 19.7 - - + +
401D GLU* 1.3 83.4 - - + +
403D ARG* 1.3 60.0 + - - +
404D GLU 3.4 0.4 - - - -
406D LEU* 3.6 14.3 - - + +
415D LEU 3.5 5.9 - - - +
417D LEU* 2.8 55.6 + - + +
418D PRO* 4.4 2.9 - - + -
601D HEM 5.2 0.9 - - + -
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Residues in contact with ARG 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 3.4 5.2 + - - +
65B SER* 3.0 33.4 + - - +
66B ASN* 2.8 39.8 + - - +
69B VAL* 3.8 6.7 - - + -
70B ARG* 3.3 50.8 - - - +
135D PRO* 3.8 2.2 - - - +
398D ALA 4.4 2.7 - - - +
399D VAL 2.9 18.6 + - - +
400D ASP* 2.9 23.4 + - - +
402D ILE* 1.3 80.0 - - - +
404D GLU* 1.3 88.5 + - - +
415D LEU 3.7 0.9 - - - -
416D ASP* 3.1 43.7 + - - +
418D PRO* 4.0 13.5 - - + -
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Residues in contact with GLU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 2.8 16.7 + - - -
70B ARG* 4.3 2.9 + - - -
135D PRO* 3.8 17.0 - - - +
136D ARG* 2.6 66.9 + - - +
400D ASP* 2.7 47.4 + - - +
403D ARG* 1.3 95.5 + - - +
405D ARG* 1.3 75.5 + - + +
414D GLY* 3.7 5.2 - - - -
415D LEU 3.5 7.2 - - - -
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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