Contacts of the helix formed by residues 79 - 90 (chain K) in PDB entry 2F8N
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 ILE 79 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1252D SER* 3.8 12.6 - - - -
1255D ALA* 3.7 5.8 - - - -
277J A 5.8 2.7 - - - +
75K LYS* 4.8 14.1 - - - +
77K ARG* 3.6 18.2 - - + +
78K ILE* 1.3 83.9 - - - +
80K PRO* 1.3 77.6 - - + +
81K ARG* 3.8 21.1 - - + +
82K HIS* 2.9 43.0 + - + +
83K LEU* 3.4 8.5 + - - +
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Residues in contact with PRO 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252D SER* 3.7 11.9 - - - +
1254D LYS* 3.8 16.8 - - + -
1255D ALA* 3.7 13.7 - - + +
1258D ILE* 3.1 34.1 - - + -
79K ILE* 1.3 86.5 - - + +
81K ARG* 1.3 66.6 + - - +
83K LEU* 3.0 5.7 + - + +
84K GLN* 2.9 22.0 + - - +
102K ILE* 4.0 3.2 - - + +
103K ALA 3.4 17.9 - - - +
104K GLN* 4.0 13.5 - - + +
105K GLY* 4.1 2.5 - - - -
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Residues in contact with ARG 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655E GLN 3.5 10.8 + - - -
656E LYS* 3.2 28.4 + - - +
657E SER 5.0 0.2 - - - -
658E THR* 3.8 21.0 - - + +
79K ILE* 3.3 15.6 - - + +
80K PRO* 1.3 78.6 - - - +
82K HIS* 1.3 64.6 + - + +
84K GLN* 3.1 2.5 - - - +
85K LEU* 2.8 59.2 + - + +
104K GLN 3.7 4.1 + - - +
105K GLY* 3.3 25.7 + - - +
106K GLY* 4.3 0.2 - - - -
107K VAL 2.3 47.9 + - - +
109K PRO* 4.8 4.9 - - - +
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Residues in contact with HIS 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K ALA* 4.0 16.6 - - + +
69K ALA* 3.9 13.3 - - + +
70K ALA* 3.5 31.7 - - + +
73K ASN* 4.2 11.5 + - + +
75K LYS* 4.0 19.1 - - + +
77K ARG 3.5 19.3 - - - -
78K ILE* 3.3 11.5 - - + -
79K ILE* 2.9 42.8 + - + +
80K PRO 3.1 0.6 - - - -
81K ARG* 1.3 82.2 - - + +
83K LEU* 1.3 61.6 + - - +
84K GLN 3.0 1.1 - - - -
85K LEU* 3.2 6.9 + - + +
86K ALA* 2.7 32.7 + - - +
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Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251D ILE* 5.4 0.9 - - + -
1255D ALA* 3.7 15.9 - - + +
1258D ILE* 3.5 44.2 - - + -
1259D MET* 3.7 19.7 - - - -
62K ILE* 3.5 21.8 - - + -
63K LEU* 5.4 2.2 - - + +
66K ALA* 3.4 25.8 - - + -
78K ILE* 4.3 7.2 - - + -
79K ILE 3.4 8.5 + - - +
80K PRO 3.0 7.8 + - - +
82K HIS* 1.3 75.7 - - - +
84K GLN* 1.3 53.6 + - - +
86K ALA* 3.6 1.1 - - - +
87K ILE* 2.7 52.1 + - + +
102K ILE* 5.0 1.3 - - + -
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Residues in contact with GLN 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K PRO 2.9 10.2 + - - +
81K ARG* 3.1 11.1 - - - +
83K LEU* 1.3 78.0 - - - +
85K LEU* 1.3 55.3 + - + +
87K ILE* 3.6 0.7 - - - +
88K ARG* 2.7 74.4 + - - +
102K ILE* 4.1 20.9 + - + +
105K GLY* 3.1 37.3 + - - +
106K GLY 3.5 17.0 + - - +
107K VAL* 4.2 12.5 - - - +
108K LEU* 4.5 0.8 - - - +
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Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ALA* 4.6 13.2 - - + +
73K ASN* 6.0 4.0 - - + +
81K ARG* 2.8 67.9 + - + +
82K HIS* 3.8 14.4 - - + +
84K GLN* 1.3 71.0 - - - +
86K ALA* 1.3 67.2 + - - +
89K ASN* 2.9 40.0 + - - +
107K VAL 5.1 0.4 - - - -
108K LEU* 3.8 21.5 - - + -
109K PRO* 4.5 9.0 - - + -
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Residues in contact with ALA 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K ILE* 4.5 4.9 - - + +
65K LEU* 3.6 21.6 - - + +
66K ALA* 3.5 31.6 - - + +
69K ALA* 4.7 2.8 - - + +
82K HIS 2.7 22.7 + - - +
83K LEU* 3.6 4.0 - - - +
85K LEU* 1.3 74.4 - - - +
87K ILE* 1.3 63.8 + - + +
89K ASN* 3.4 8.0 + - - +
90K ASP* 3.4 17.0 + - - +
93K LEU* 5.4 1.3 - - + -
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Residues in contact with ILE 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258D ILE* 5.6 2.7 - - + -
298F TYR* 6.0 0.4 - - + -
62K ILE* 4.6 21.3 - - + -
83K LEU* 2.7 35.8 + - + +
84K GLN* 3.7 2.9 - - - +
86K ALA* 1.3 73.6 - - - +
88K ARG* 1.3 87.9 + - - +
89K ASN 3.3 0.5 + - - -
90K ASP 3.4 9.0 + - - +
93K LEU* 3.9 22.0 - - + +
94K ASN* 3.4 15.9 + - - +
97K LEU* 3.6 31.9 - - + -
102K ILE* 3.2 30.7 - - + -
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Residues in contact with ARG 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K GLN* 2.7 52.2 + - - +
87K ILE* 1.3 87.5 - - - +
89K ASN* 1.3 58.9 + - - +
90K ASP 3.5 0.4 - - - -
94K ASN* 2.9 39.9 + - - +
97K LEU* 2.8 28.1 + - - +
98K GLY* 4.2 5.2 + - - -
100K VAL* 3.1 30.1 + - - +
101K THR* 4.8 1.2 - - - +
102K ILE* 4.2 14.1 - - - +
107K VAL* 6.0 0.2 - - - -
108K LEU* 3.4 38.0 - - + +
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Residues in contact with ASN 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K LEU* 2.9 33.2 + - - +
86K ALA* 4.2 2.9 - - - +
87K ILE 3.2 0.4 - - - -
88K ARG* 1.3 78.2 - - - +
90K ASP* 1.3 59.2 + - - +
91K GLU 3.8 2.9 + - - -
108K LEU* 3.4 30.9 - - - +
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Residues in contact with ASP 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303D LEU* 5.1 1.0 - - - +
61K GLU* 5.8 0.7 - - - +
65K LEU* 4.1 19.9 - - + +
86K ALA 3.4 15.4 + - - +
87K ILE 3.4 0.8 + - - -
88K ARG 5.1 0.2 - - - -
89K ASN* 1.3 76.9 - - - +
91K GLU* 1.3 69.2 + - - +
92K GLU* 3.0 10.1 + - - +
93K LEU* 2.7 44.3 + - + +
94K ASN* 2.9 22.8 + - - +
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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