Contacts of the helix formed by residues 393 - 403 (chain D) in PDB entry 5NSS
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 THR 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391D ALA* 4.5 0.8 - - - +
392D THR* 1.3 93.0 + - - +
394D ILE* 1.3 66.9 + - - +
395D LYS* 3.8 7.8 + - - +
396D ALA* 2.9 18.5 + - - +
397D ALA* 2.9 22.3 + - - +
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Residues in contact with ILE 394 (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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1305C TYR* 4.9 13.0 - - - +
1309C VAL* 5.6 10.3 - - + -
382D TYR* 4.8 12.7 - - + -
393D THR* 1.3 73.8 - - - +
395D LYS* 1.3 56.4 + - - +
397D ALA* 3.3 8.2 + - - +
398D LYS* 2.9 51.2 + - + +
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Residues in contact with LYS 395 (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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393D THR* 3.2 8.1 + - - +
394D ILE* 1.3 77.7 - - - +
396D ALA* 1.3 58.7 + - - +
398D LYS* 3.2 15.3 + - + +
399D LYS* 2.9 26.9 + - - +
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Residues in contact with ALA 396 (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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391D ALA* 4.7 2.0 - - + -
392D THR* 3.3 31.4 - - - +
393D THR* 2.9 14.7 + - - +
395D LYS* 1.3 78.1 - - - +
397D ALA* 1.3 57.7 + - - +
399D LYS* 3.1 9.7 + - - +
400D MET* 2.9 32.4 + - + +
403D ARG* 4.4 0.9 + - - -
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Residues in contact with ALA 397 (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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382D TYR* 3.6 26.7 - - + +
385D LEU* 3.8 26.2 - - + -
391D ALA* 4.1 11.1 - - + +
393D THR 2.9 11.3 + - - +
394D ILE* 3.6 9.2 - - - +
396D ALA* 1.3 73.2 - - - +
398D LYS* 1.3 60.9 + - - +
400D MET* 3.1 3.5 + - - +
401D VAL* 2.9 32.7 + - - +
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Residues in contact with LYS 398 (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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1305C TYR* 4.7 8.5 + - - -
378D LYS* 5.8 0.4 - - - +
382D TYR* 3.4 43.5 + - + +
394D ILE* 2.9 37.2 + - + +
395D LYS* 3.2 14.8 + - + +
397D ALA* 1.3 76.3 - - - +
399D LYS* 1.3 56.7 + - - +
401D VAL* 3.4 1.4 + - - +
402D GLU* 2.9 45.2 + - - +
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Residues in contact with LYS 399 (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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395D LYS 2.9 13.1 + - - +
396D ALA* 3.1 12.5 + - - +
398D LYS* 1.3 77.0 - - - +
400D MET* 1.3 56.3 + - - +
402D GLU* 3.8 8.4 - - - +
403D ARG* 2.9 54.2 + - + +
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Residues in contact with MET 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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385D LEU* 3.9 28.0 - - + -
390D LEU* 4.4 16.4 - - + +
391D ALA* 3.7 33.4 - - - -
396D ALA* 2.9 17.2 + - + +
397D ALA* 3.1 7.4 + - - +
399D LYS* 1.3 75.9 - - - +
401D VAL* 1.3 60.5 + - - +
403D ARG* 3.3 22.6 + - - +
404D GLU 3.6 11.8 + - - -
405D GLU* 3.4 36.3 + - - +
407D VAL* 5.5 5.8 - - + -
408D VAL* 3.8 12.0 - - + +
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Residues in contact with VAL 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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374D LEU* 5.0 15.2 - - + +
378D LYS* 3.4 35.2 - - + +
381D ILE* 3.7 31.2 - - + -
382D TYR* 3.6 17.0 - - + -
385D LEU* 4.9 3.4 - - + -
397D ALA 2.9 19.7 + - - +
398D LYS 3.9 3.1 - - - +
400D MET* 1.3 76.2 - - - +
402D GLU* 1.3 64.2 + - - +
404D GLU* 3.1 19.8 + - - +
408D VAL* 4.7 10.3 - - + -
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Residues in contact with GLU 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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378D LYS* 5.2 9.4 - - - +
382D TYR* 5.6 0.2 - - - +
398D LYS* 2.9 32.8 + - + +
399D LYS* 4.0 6.2 - - - +
401D VAL* 1.3 75.8 - - - +
403D ARG* 1.3 62.4 + - + +
404D GLU* 3.5 8.5 + - - +
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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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396D ALA 4.4 0.8 + - - -
399D LYS* 2.9 32.4 + - - +
400D MET* 3.3 29.9 - - - +
401D VAL 3.2 0.4 - - - -
402D GLU* 1.3 76.3 - - + +
404D GLU* 1.3 72.2 + - - +
405D GLU* 3.0 33.5 + - + +
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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