Contacts of the helix formed by residues 89 - 100 (chain K) in PDB entry 4E45
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 SER 89 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86K ALA 3.3 5.6 + - - +
87K ARG 3.2 1.8 - - - -
88K ARG* 1.3 81.3 - - - +
90K ASN* 1.3 54.0 + - - +
91K SER* 3.1 13.3 + - - -
92K LEU* 3.0 22.4 + - - +
93K LEU* 2.7 34.6 + - - +
80L ASP 5.2 0.4 + - - -
708O VAL* 3.7 11.4 - - - +
710O PHE* 3.4 35.5 - - - -
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Residues in contact with ASN 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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87K ARG 5.3 2.6 - - - +
88K ARG 4.3 0.9 + - - +
89K SER* 1.3 70.6 + - - +
91K SER* 1.3 59.0 + - - +
93K LEU* 3.1 10.4 + - - +
94K LYS* 2.8 31.6 + - - +
63M LYS* 5.5 7.2 + - - +
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Residues in contact with SER 91 (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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89K SER* 3.1 13.0 + - - -
90K ASN* 1.3 78.3 - - - +
92K LEU* 1.3 60.5 + - - +
94K LYS* 4.0 5.5 - - - +
95K TYR* 3.2 18.9 + - - +
710O PHE* 4.4 11.6 + - - +
713O LEU* 3.4 21.5 - - - +
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Residues in contact with LEU 92 (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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86K ALA* 3.7 30.1 - - + +
89K SER* 3.0 23.7 + - - +
91K SER* 1.3 72.6 - - - +
93K LEU* 1.3 66.2 + - - +
95K TYR* 3.4 2.4 + - + -
96K ILE* 3.0 36.6 + - + +
41L LEU* 4.4 3.8 - - + -
44L VAL* 3.6 31.4 - - + -
80L ASP 4.5 5.4 - - - +
81L PHE* 3.6 27.6 - - + -
710O PHE* 3.9 20.9 - - + -
713O LEU* 3.7 11.3 - - + +
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Residues in contact with LEU 93 (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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83K LYS* 3.5 35.4 - - + +
86K ALA* 3.6 14.7 + - + +
87K ARG* 4.7 7.4 - - + +
89K SER 2.7 20.9 + - - +
90K ASN* 3.7 9.9 - - - +
92K LEU* 1.3 73.6 - - - +
94K LYS* 1.3 53.9 + - - +
96K ILE* 3.6 0.4 + - + -
97K THR* 2.6 48.8 + - - +
67M MET* 4.6 23.3 - - + -
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Residues in contact with LYS 94 (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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90K ASN 2.8 18.8 + - - +
91K SER* 4.0 7.0 - - - +
93K LEU* 1.3 73.8 - - - +
95K TYR* 1.3 57.3 + - - +
97K THR* 3.4 4.6 + - - -
98K ASP* 2.9 41.6 + - - +
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Residues in contact with TYR 95 (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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91K SER 3.2 18.3 + - - +
92K LEU* 4.0 3.6 - - + +
94K LYS* 1.3 76.0 - - - +
96K ILE* 1.3 76.8 + - + +
98K ASP* 3.5 6.6 + - - +
99K LYS* 3.0 63.2 + - + +
40L GLU* 4.3 6.1 + - + -
43L LYS* 6.1 1.4 - - - +
44L VAL* 3.2 34.4 - - + +
713O LEU* 3.7 26.0 - - + -
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Residues in contact with ILE 96 (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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82K VAL* 4.6 6.5 - - + +
83K LYS* 4.3 14.8 - - + -
86K ALA* 4.1 13.0 - - + -
92K LEU* 3.0 28.8 + - + +
93K LEU* 4.2 2.2 - - + +
95K TYR* 1.3 95.8 - - + +
97K THR* 1.3 59.0 + - - +
99K LYS* 3.7 2.0 + - + -
100K SER* 3.1 25.8 + - - -
37L LEU* 3.6 27.2 - - + +
40L GLU* 4.6 6.3 - - + -
41L LEU* 4.0 45.8 - - + +
44L VAL* 4.9 0.9 - - + -
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Residues in contact with THR 97 (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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83K LYS* 3.7 34.5 + - + +
93K LEU* 2.6 37.8 + - - +
94K LYS* 3.8 6.1 - - - -
96K ILE* 1.3 74.7 - - - +
98K ASP* 1.3 66.9 + - - +
100K SER* 3.3 13.5 - - - -
101K GLU* 3.4 24.8 + - - +
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Residues in contact with ASP 98 (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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94K LYS* 2.9 25.8 + - - +
95K TYR* 3.5 6.9 + - - +
97K THR* 1.3 78.4 - - - +
99K LYS* 1.3 66.6 + - + +
100K SER 3.1 1.1 - - - -
101K GLU* 3.0 23.3 + - - +
102K GLU* 3.2 22.9 + - - +
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Residues in contact with LYS 99 (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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95K TYR* 3.0 63.2 + - + +
96K ILE* 3.7 5.1 + - - +
98K ASP* 1.3 74.8 - - + +
100K SER* 1.3 60.9 + - - +
101K GLU 3.2 0.2 - - - -
102K GLU* 3.3 41.6 + - + +
37L LEU* 4.1 12.6 - - + +
40L GLU* 3.3 35.8 + - + +
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Residues in contact with SER 100 (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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79K THR* 4.0 17.0 + - - +
83K LYS* 4.4 11.1 - - - -
96K ILE 3.1 19.6 + - - -
97K THR* 3.3 13.0 - - - -
98K ASP 3.1 0.4 - - - -
99K LYS* 1.3 77.6 - - - +
101K GLU* 1.3 59.0 + - - +
102K GLU 4.2 3.3 - - - +
37L LEU* 3.8 26.2 - - - +
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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