Contacts of the helix formed by residues 69 - 79 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ALA 3.9 0.4 + - - -
68G LEU* 1.3 76.2 - - - +
70G GLU* 1.3 61.6 + - - +
71G ASN* 3.4 6.7 - - + +
72G LEU* 3.7 11.5 - - + +
73G LEU* 2.9 26.9 + - - +
71J ASN* 3.7 26.6 - - + +
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Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN* 1.3 75.4 - - - +
71G ASN* 1.3 54.9 + - - +
73G LEU* 5.2 0.4 - - - -
74G ASP* 2.6 42.3 + - + +
113G PRO* 5.5 12.8 - - + -
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Residues in contact with ASN 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN* 4.3 3.2 - - + +
70G GLU* 1.3 76.8 - - - +
72G LEU* 1.3 59.8 + - - +
74G ASP* 4.7 0.9 - - - -
75G SER* 2.6 40.7 + - - +
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G LEU* 3.7 10.8 - - + -
69G ASN* 3.5 24.1 + - + +
70G GLU 3.4 0.4 - - - -
71G ASN* 1.3 78.6 - - - +
73G LEU* 1.3 53.8 + - - +
75G SER* 4.9 0.2 - - - -
76G GLU* 2.7 39.7 + - - +
71J ASN* 5.7 2.2 - - + -
75J SER* 5.7 9.6 - - - -
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G ASN 5.5 0.2 - - - +
65G CYS* 4.2 21.1 - - + +
68G LEU* 3.6 16.4 - - + +
69G ASN 2.9 17.1 + - - +
70G GLU* 5.2 0.2 - - - -
72G LEU* 1.3 75.5 - - - +
74G ASP* 1.3 60.2 + - - +
76G GLU* 4.5 2.2 - - - -
77G LEU* 2.9 34.8 + - - +
112G ALA* 5.6 3.6 - - + -
116G VAL* 4.5 9.4 - - + +
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Residues in contact with ASP 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G GLU* 2.6 24.1 + - + +
71G ASN* 4.7 1.6 - - - -
73G LEU* 1.3 77.3 - - - +
75G SER* 1.3 55.5 + - - +
78G PHE* 2.7 41.0 + - + +
115G MET* 5.0 15.0 - - + -
116G VAL* 4.5 15.7 - - + +
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Residues in contact with SER 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ASN* 2.6 26.3 + - - -
72G LEU* 4.6 0.7 - - - -
74G ASP* 1.3 76.4 - - - +
76G GLU* 1.3 59.8 + - - +
79G GLY* 2.9 37.3 + - - +
80G HIS* 3.7 10.8 + - - +
92G HIS* 5.6 0.2 - - - +
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Residues in contact with GLU 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G LEU 2.7 22.9 + - - +
73G LEU* 4.2 3.1 - - - +
75G SER* 1.3 78.5 - - - +
77G LEU* 1.3 61.2 + - - +
79G GLY* 3.9 5.4 + - - -
92G HIS* 5.0 9.8 - - - +
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G LEU 2.9 19.1 + - - +
76G GLU* 1.3 78.7 - - - +
78G PHE* 1.3 61.6 + - - +
79G GLY* 3.6 0.5 + - - -
116G VAL* 4.9 17.3 - - + +
119G LYS* 5.5 2.6 - - + +
120G LEU* 5.3 12.5 - - + +
123G VAL* 5.6 5.7 - - - +
129G LEU* 5.5 6.2 - - - +
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Residues in contact with PHE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ASP* 2.7 24.4 + - + +
77G LEU* 1.3 77.7 - - - +
79G GLY* 1.3 60.4 + - - +
119G LYS* 3.8 29.1 - - + +
129G LEU* 6.1 0.7 - - - -
130G GLU* 3.2 29.5 + - - +
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Residues in contact with GLY 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G SER* 2.9 26.4 + - - +
76G GLU 3.9 1.9 + - - -
77G LEU 3.3 3.6 + - - -
78G PHE* 1.3 82.6 - - - +
80G HIS* 1.3 59.5 + - - -
92G HIS* 3.7 16.6 - - - -
129G LEU* 6.0 0.9 - - - -
130G GLU 3.3 14.4 - - - -
132G 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