Contacts of the helix formed by residues 91 - 105 (chain O) in PDB entry 5L4K
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 91 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89O ASP* 3.3 0.6 - - + +
90O PRO* 1.3 102.3 + - - +
92O VAL* 1.3 65.5 + - + +
93O ALA 3.4 0.7 - - - -
94O LEU* 3.9 12.4 - - + +
95O THR* 3.1 27.2 + - - +
125O ILE* 5.0 7.5 - - - +
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Residues in contact with VAL 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87O MET* 4.6 11.2 - - + -
89O ASP* 3.9 28.0 - - + +
91O ASN* 1.3 78.7 - - + +
93O ALA* 1.3 60.8 + - - +
95O THR* 3.5 4.3 + - - -
96O PHE* 2.9 30.7 + - + +
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Residues in contact with ALA 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O VAL* 3.7 25.4 - - + +
87O MET* 3.8 15.3 - - + -
89O ASP 3.4 19.8 + - - +
92O VAL* 1.3 77.7 - - - +
94O LEU* 1.3 59.3 + - - +
96O PHE* 3.9 6.5 - - - -
97O LEU* 2.9 36.3 + - - +
121O LEU* 4.2 13.7 - - + -
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Residues in contact with LEU 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O PRO 3.5 23.2 + - - +
91O ASN* 3.9 13.3 + - + +
92O VAL 3.4 0.6 - - - -
93O ALA* 1.3 78.9 - - - +
95O THR* 1.3 68.2 + - + +
97O LEU* 3.2 3.9 + - - +
98O GLU* 3.0 46.6 + - - +
118O ILE* 4.4 11.3 - - + +
121O LEU* 4.5 14.0 - - + +
122O LYS* 3.8 39.3 - - + -
125O ILE* 5.4 6.3 - - + -
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Residues in contact with THR 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ASN 3.1 18.4 + - - +
92O VAL* 3.5 7.3 + - - +
94O LEU* 1.3 84.0 - - + +
96O PHE* 1.3 62.8 + - - +
98O GLU* 4.0 12.5 - - + +
99O LYS* 2.9 31.2 + - - +
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Residues in contact with PHE 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O TYR* 3.7 41.5 - + - -
80O ILE* 3.7 30.3 - - + -
83O VAL* 3.8 24.5 - - + -
84O VAL* 3.9 13.7 - - + -
87O MET* 3.7 20.2 - - + -
92O VAL* 2.9 24.7 + - + +
93O ALA* 3.7 3.4 - - - +
94O LEU 3.3 0.2 - - - -
95O THR* 1.3 77.7 + - - +
97O LEU* 1.3 57.8 + - - +
99O LYS* 3.5 22.0 + - - +
100O THR* 3.0 36.5 + - - -
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Residues in contact with LEU 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O VAL* 5.9 4.3 - - + -
80O ILE* 3.8 32.1 - - + +
81O LEU* 5.3 1.8 - - + +
84O VAL* 4.2 18.6 - - + -
93O ALA 2.9 20.8 + - - +
94O LEU* 3.7 4.0 - - - +
96O PHE* 1.3 75.7 - - + +
98O GLU* 1.3 60.7 + - - +
100O THR* 3.2 7.5 + - + -
101O ARG* 2.8 27.4 + - - +
114O CYS* 5.2 9.8 - - + +
117O ALA* 3.9 35.0 - - + -
118O ILE* 4.0 14.9 - - + +
121O LEU* 3.9 23.3 - - + -
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Residues in contact with GLU 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O LEU* 3.0 46.3 + - + +
95O THR* 4.0 11.5 + - - +
97O LEU* 1.3 72.9 - - - +
99O LYS* 1.3 60.2 + - - +
101O ARG* 2.8 52.0 + - - +
102O GLU* 3.1 19.0 + - + +
118O ILE* 3.9 14.6 - - + -
122O LYS* 5.1 5.3 - - - -
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Residues in contact with LYS 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O TYR* 5.1 2.0 + - - -
95O THR 2.9 20.1 + - - +
96O PHE* 3.6 35.3 + - - +
98O GLU* 1.3 76.5 - - - +
100O THR* 1.3 66.5 + - - +
102O GLU* 3.7 5.0 + - - +
103O LYS* 3.6 47.3 + - + +
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Residues in contact with THR 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O TYR* 4.9 1.7 + - - -
77O VAL* 4.7 6.5 - - + -
80O ILE* 3.5 41.4 - - + +
96O PHE* 3.0 26.9 + - - -
97O LEU* 3.4 13.0 - - + +
98O GLU 3.1 0.2 - - - -
99O LYS* 1.3 77.6 + - - +
101O ARG* 1.3 59.8 + - - +
103O LYS* 3.0 13.7 + - - +
104O VAL* 2.9 47.3 + - + +
114O CYS* 5.1 3.4 - - - -
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Residues in contact with ARG 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O LEU 2.8 12.7 + - - +
98O GLU* 2.8 42.3 + - - +
100O THR* 1.3 71.8 - - - +
102O GLU* 1.3 74.8 + - - +
104O VAL* 3.7 8.2 - - - +
105O LYS* 2.9 40.1 + - + +
111O VAL* 5.1 3.6 - - + -
114O CYS* 4.0 18.2 - - + -
115O LYS* 3.9 40.8 - - + +
118O ILE* 3.5 28.2 - - + +
122O LYS* 5.4 3.2 - - - +
134O THR* 6.1 1.8 - - - +
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Residues in contact with GLU 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98O GLU* 3.1 13.2 + - + +
99O LYS* 4.4 5.2 - - - +
100O THR 3.2 0.2 - - - -
101O ARG* 1.3 113.6 + - - +
103O LYS* 1.3 60.3 + - + +
105O LYS* 3.2 32.0 + - - +
106O SER* 3.2 23.9 + - - -
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Residues in contact with LYS 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O TYR* 4.9 8.9 + - - -
68O GLU* 4.0 29.2 + - + +
99O LYS* 3.6 47.0 + - + +
100O THR* 3.0 11.6 + - - +
102O GLU* 1.3 79.7 - - + +
104O VAL* 1.3 63.6 + - + +
105O LYS 3.6 0.2 - - - -
106O SER* 4.3 6.0 - - - -
107O SER* 2.8 21.3 + - - -
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Residues in contact with VAL 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O PRO* 4.2 14.5 - - + +
76O LEU* 4.0 24.9 - - + -
77O VAL* 4.1 9.9 - - + -
100O THR* 2.9 34.2 + - + +
101O ARG* 3.7 5.8 - - - +
103O LYS* 1.3 80.4 - - + +
105O LYS* 1.3 63.1 + - - +
106O SER 3.3 1.3 - - - -
107O SER* 3.0 21.3 + - - +
108O ASP* 3.1 10.2 + - - -
109O GLU* 4.2 8.6 + - - +
111O VAL* 4.1 8.1 - - + +
114O CYS* 3.7 28.5 - - - -
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Residues in contact with LYS 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O ARG* 2.9 20.8 + - + +
102O GLU* 3.2 37.4 + - - +
104O VAL* 1.3 74.4 - - - +
106O SER* 1.3 66.3 + - - +
108O ASP* 3.4 15.0 + - - +
109O GLU 4.8 1.4 + - - +
111O VAL* 3.6 32.8 - - + -
115O LYS* 4.9 8.3 - - - +
141O MET* 4.8 13.5 - - + -
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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