Contacts of the helix formed by residues 77 - 87 (chain B) 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 ASP 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B SER 5.3 3.6 - - - +
76B GLU* 1.3 74.7 - - - +
78B ILE* 1.3 83.9 + - - +
79B LEU* 3.9 22.2 - - - +
80B GLU* 2.7 33.3 + - + +
81B ILE* 2.9 12.1 + - - +
569D LEU* 6.2 0.3 - - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 5.6 17.7 - - + -
67B GLU* 3.2 31.6 - - + +
68B TYR* 4.9 2.5 - - - -
69B SER* 3.3 32.1 - - - +
74B VAL* 5.9 3.8 - - + -
76B GLU 3.6 3.1 + - - +
77B ASP* 1.3 87.3 + - - +
79B LEU* 1.3 87.2 + - + +
81B ILE* 3.3 14.9 + - + +
82B LEU* 2.9 42.3 + - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 6.4 1.3 - - + -
77B ASP* 3.1 17.1 + - - +
78B ILE* 1.3 95.7 - - + +
80B GLU* 1.3 58.6 + - - +
82B LEU* 3.6 15.8 + - + +
83B LEU* 2.9 25.6 + - - +
86B LYS* 5.9 0.2 - - - -
526D VAL* 5.4 15.7 - - + +
569D LEU* 6.5 1.1 - - + -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 3.2 25.4 - - + +
77B ASP* 2.7 25.9 + - + +
79B LEU* 1.3 71.7 - - - +
81B ILE* 1.3 53.8 + - - -
83B LEU* 3.2 8.6 + - - +
84B ASN* 2.6 38.3 + - - +
551D ARG* 4.1 20.4 - - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 5.6 9.4 - - + -
74B VAL* 4.5 11.9 - - + -
76B GLU* 3.3 42.6 - - + +
77B ASP 2.9 29.5 + - - +
78B ILE* 3.7 12.6 - - + +
80B GLU* 1.3 75.3 - - - +
82B LEU* 1.3 60.1 + - + +
84B ASN* 3.2 4.2 + - - +
85B LEU* 2.9 39.3 + - + +
130B ILE* 3.8 28.7 - - + +
131B CYS* 4.2 10.5 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 3.8 40.6 - - + -
61B ILE* 4.4 13.7 - - + -
78B ILE* 2.9 28.3 + - + +
79B LEU* 3.8 22.0 - - + +
81B ILE* 1.3 76.8 - - + +
83B LEU* 1.3 57.5 + - - +
85B LEU* 3.4 7.2 + - + +
86B LYS* 2.9 38.8 + - - +
173B VAL* 4.5 20.4 - - + -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 2.9 16.2 + - - +
80B GLU* 3.4 11.7 - - - +
81B ILE 3.2 0.4 - - - -
82B LEU* 1.3 77.2 - - - +
84B ASN* 1.3 67.1 + - - +
86B LYS* 3.2 14.0 + - - +
87B GLY* 2.9 24.6 + - - -
526D VAL* 4.3 17.7 - - + +
528D THR* 4.3 25.6 - - + +
551D ARG* 4.3 28.3 - - - +
569D LEU* 6.2 0.4 - - + -
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU* 2.7 22.6 + - - -
80B GLU* 2.6 29.3 + - - +
81B ILE 3.6 5.2 - - - +
83B LEU* 1.3 85.1 - - - +
85B LEU* 1.3 62.1 + - - +
87B GLY* 3.4 10.5 + - - +
88B LEU* 3.8 10.9 + - - +
128B HIS* 5.8 2.8 - - - +
129B VAL 3.0 29.9 - - - +
130B ILE* 3.4 18.1 + - - +
551D ARG* 6.1 0.2 - - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 4.1 13.3 - - + +
59B VAL* 3.6 43.1 - - + -
81B ILE* 2.9 33.1 + - + +
82B LEU* 3.7 10.8 - - + +
84B ASN* 1.3 76.4 - - - +
86B LYS* 1.3 61.9 + - + +
88B LEU* 3.3 29.9 + - + +
102B LEU* 5.3 7.0 - - + -
115B ILE* 5.8 4.0 - - + -
130B ILE* 3.7 32.1 - - + -
144B ILE* 4.6 16.6 - - + +
173B VAL* 6.2 0.7 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 5.3 6.3 - - + -
82B LEU* 2.9 25.0 + - - +
83B LEU* 3.2 12.3 + - - +
85B LEU* 1.3 72.7 - - + +
87B GLY* 1.3 56.5 + - - +
88B LEU 3.1 13.7 + - - +
152B TYR* 5.5 0.2 + - - -
173B VAL* 4.0 17.2 - - + +
174B ASP* 3.2 53.9 + - + +
176B CYS* 5.9 2.4 - - - +
526D VAL* 3.3 33.1 - - - +
527D LEU* 5.4 10.5 - - + +
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 2.9 15.4 + - - -
84B ASN* 3.4 6.9 + - - -
85B LEU 3.2 1.0 - - - -
86B LYS* 1.3 75.5 - - - +
88B LEU* 1.3 58.3 + - - +
89B ALA 4.3 0.5 + - - -
125B LYS* 5.7 5.9 + - - +
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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