Contacts of the helix formed by residues 69 - 79 (chain L) 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 ASN 69 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L ALA 3.9 0.6 + - - -
68L LEU* 1.3 76.9 - - - +
70L GLU* 1.3 62.5 + - - +
71L ASN* 3.4 6.3 - - + +
72L LEU* 3.7 12.5 - - + +
73L LEU* 2.9 27.4 + - - +
115N MET* 5.5 1.4 - - - +
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Residues in contact with GLU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ASN* 1.3 76.7 - - - +
71L ASN* 1.3 54.4 + - - +
73L LEU* 5.2 0.4 - - - -
74L ASP* 2.6 41.2 + - + +
113L PRO* 5.5 13.2 - - + -
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Residues in contact with ASN 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ASN* 3.4 3.4 - - + +
70L GLU* 1.3 78.0 - - - +
72L LEU* 1.3 58.3 + - - +
74L ASP* 4.7 0.9 - - - -
75L SER* 2.6 40.5 + - - +
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Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68L LEU* 3.7 10.8 - - + -
69L ASN* 3.5 23.9 + - + +
70L GLU 3.4 0.2 - - - -
71L ASN* 1.3 79.8 - - - +
73L LEU* 1.3 51.6 + - - +
75L SER* 4.6 0.8 - - - -
76L GLU* 2.7 40.0 + - - +
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L ASN 5.5 0.2 - - - +
65L CYS* 4.2 20.4 - - + +
68L LEU* 3.6 17.0 - - + +
69L ASN 2.9 17.0 + - - +
70L GLU* 4.8 0.4 - - - +
72L LEU* 1.3 75.2 - - - +
74L ASP* 1.3 62.1 + - - +
76L GLU* 4.5 2.7 - - - -
77L LEU* 2.9 34.9 + - + +
112L ALA* 5.6 3.8 - - + -
116L VAL* 4.5 11.1 - - + +
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Residues in contact with ASP 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ALA 5.9 1.8 - - - +
70L GLU* 2.6 25.0 + - + +
71L ASN* 4.7 1.1 - - - -
73L LEU* 1.3 77.7 - - - +
75L SER* 1.3 54.1 + - - +
78L PHE* 2.7 41.6 + - + +
113L PRO* 6.6 0.2 - - + -
115L MET* 5.0 14.6 - - + -
116L VAL* 4.5 15.6 - - + +
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Residues in contact with SER 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ASN* 2.6 26.5 + - - +
72L LEU* 4.6 0.4 - - - -
74L ASP* 1.3 75.3 - - - +
76L GLU* 1.3 60.2 - - - +
78L PHE* 4.8 0.2 - - - -
79L GLY 2.9 37.4 + - - +
80L HIS* 3.7 10.7 + - - +
92L HIS* 5.6 0.2 - - - +
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Residues in contact with GLU 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L LEU 2.7 24.0 + - - +
73L LEU* 4.2 2.5 - - - +
75L SER* 1.3 79.4 - - - +
77L LEU* 1.3 62.1 + - - +
79L GLY* 3.9 5.2 + - - -
92L HIS* 5.0 10.0 - - - +
95L ARG* 5.9 2.4 - - - +
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L LEU* 2.9 19.3 + - + +
76L GLU* 1.3 76.6 - - - +
78L PHE* 1.3 62.6 + - - +
79L GLY 3.6 0.2 + - - -
116L VAL* 4.9 17.5 - - + +
119L LYS* 5.5 2.2 - - + +
120L LEU* 5.3 12.1 - - + +
123L VAL* 5.6 5.7 - - - +
129L LEU* 5.5 6.4 - - - +
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Residues in contact with PHE 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ALA* 3.8 26.4 - - + +
74L ASP* 2.7 23.7 + - + +
77L LEU* 1.3 78.3 - - - +
79L GLY* 1.3 61.0 + - - +
116L VAL* 6.1 0.2 - - - -
119L LYS* 3.8 24.0 - - + -
123L VAL* 6.3 1.6 - - - -
129L LEU* 6.1 0.4 - - - -
130L GLU* 3.2 29.3 + - - +
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Residues in contact with GLY 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L SER* 2.9 26.3 + - - +
76L GLU 3.9 1.3 + - - -
77L LEU 3.3 3.6 - - - -
78L PHE* 1.3 82.9 - - - +
80L HIS* 1.3 59.8 + - - -
92L HIS* 3.7 16.4 - - - -
129L LEU* 6.0 0.9 - - - -
130L GLU 3.3 14.6 - - - -
131L ARG* 5.5 0.2 - - - -
132L VAL 5.9 0.2 - - - -
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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