Contacts of the helix formed by residues 92 - 110 (chain A) in PDB entry 5A36
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 MET 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY* 3.2 1.8 - - - -
91A LYS* 1.3 80.7 - - - +
93A ARG* 1.3 66.7 + - - +
94A PHE* 3.1 30.1 - - + -
95A HIS* 3.0 37.6 + - + +
96A LYS* 3.5 4.3 + - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS 3.3 4.0 + - - -
92A MET* 1.3 72.8 - - - +
94A PHE* 1.3 61.0 + - - +
96A LYS* 3.2 13.8 + - + +
97A ILE* 3.1 41.0 + - + +
120A GLU* 3.9 19.8 + - - +
123A VAL* 4.0 17.3 + - + +
124A ASP* 2.7 34.8 + - - -
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASP* 4.4 4.3 - - - -
92A MET* 3.1 32.5 - - + -
93A ARG* 1.3 79.3 - - - +
95A HIS* 1.3 98.1 + + - +
97A ILE* 3.7 10.4 - - + +
98A ALA* 3.0 26.1 + - + +
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASP* 2.8 37.4 + - + +
89A ARG 3.5 23.5 + - - +
90A GLY* 3.4 24.6 - - - +
92A MET* 3.0 35.7 + - + +
94A PHE* 1.3 107.6 - + - +
96A LYS* 1.3 64.1 + - - +
98A ALA* 3.3 1.4 + - - +
99A ASN* 3.0 31.2 + - - +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 3.6 20.9 - - + +
68A ASN* 3.7 33.8 - - + +
90A GLY 5.2 2.7 - - - +
91A LYS* 3.5 30.5 + - - +
92A MET 3.5 6.0 + - - +
93A ARG* 3.2 14.2 + - + +
95A HIS* 1.3 75.7 - - - +
97A ILE* 1.3 57.2 + - - +
99A ASN* 3.3 2.5 + - - +
100A VAL* 3.0 34.1 + - - +
123A VAL* 3.8 16.8 - - + -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG* 3.3 33.2 - - + +
94A PHE* 3.7 13.0 - - - +
96A LYS* 1.3 78.1 - - - +
98A ALA* 1.3 57.7 + - - +
100A VAL 3.7 0.2 + - - -
101A ASN* 3.0 50.1 + - - +
119A ALA* 3.8 7.2 - - + +
120A GLU* 3.6 38.6 - - + +
123A VAL* 3.6 25.4 - - + -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 3.4 31.9 - - - +
94A PHE* 3.0 18.7 + - + +
95A HIS 3.8 0.7 - - - +
96A LYS 3.3 0.6 - - - -
97A ILE* 1.3 75.9 - - - +
99A ASN* 1.3 58.8 + - - +
101A ASN* 3.5 7.9 + - - +
102A LYS* 3.1 35.8 + - - +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN 3.3 26.4 + - - +
69A GLY* 3.9 6.5 - - - -
70A LEU* 3.7 12.6 - - - +
73A MET* 3.6 23.0 - - - +
87A PRO* 3.6 5.9 - - - +
88A ASP* 2.7 47.2 + - - +
95A HIS* 3.0 20.5 + - - +
96A LYS* 3.6 0.9 - - - +
98A ALA* 1.3 76.4 - - - +
100A VAL* 1.3 65.3 + - - +
102A LYS* 3.3 10.1 + - - +
103A ALA* 3.1 17.3 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE 4.0 9.6 - - - +
69A GLY* 3.6 23.3 - - - +
72A LEU* 4.5 7.4 - - + -
96A LYS 3.0 17.4 + - - +
97A ILE 4.1 0.2 - - - +
99A ASN* 1.3 72.7 - - - +
101A ASN* 1.3 60.5 + - - +
103A ALA* 3.2 6.4 + - - +
104A LEU* 2.9 39.2 + - + +
119A ALA* 3.7 30.3 - - + -
122A ILE* 4.0 20.2 - - + -
123A VAL* 4.0 14.6 - - + -
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.0 41.7 + - - +
98A ALA* 3.8 7.9 - - - +
99A ASN 3.2 0.4 - - - -
100A VAL* 1.3 76.6 - - - +
102A LYS* 1.3 51.8 + - + +
104A LEU* 3.4 7.3 + - - +
105A ASP* 2.8 48.9 + - - +
119A ALA* 3.2 18.4 + - - +
120A GLU* 4.6 5.4 + - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 4.2 15.7 - - + -
84A LEU* 4.2 5.0 - - + +
85A PRO* 4.0 28.4 - - + +
86A LYS 2.8 28.9 + - - +
88A ASP* 2.7 35.8 + - - +
98A ALA* 3.1 22.0 + - - +
99A ASN* 3.5 10.5 + - - +
100A VAL 3.2 0.4 - - - -
101A ASN* 1.3 74.8 - - - +
103A ALA* 1.3 64.0 + - - +
105A ASP* 4.1 5.9 - - - +
106A TYR* 3.1 24.3 + - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.5 39.0 - - + -
73A MET* 4.2 8.3 - - + +
76A LEU* 3.5 18.0 - - + +
84A LEU* 4.4 4.9 - - - -
99A ASN 3.1 12.9 + - - +
100A VAL 3.2 4.5 + - - +
102A LYS* 1.3 75.6 - - - +
104A LEU* 1.3 57.8 + - + +
106A TYR* 3.3 2.6 + - - +
107A ILE* 3.2 33.9 + - + +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 2.9 31.0 + - + +
101A ASN* 3.9 7.9 - - - +
103A ALA* 1.3 74.2 - - + +
105A ASP* 1.3 66.9 + - - +
107A ILE* 3.5 9.8 + - + +
108A ALA* 3.0 23.6 + - - +
114A LEU* 3.8 30.4 - - + +
117A ILE* 4.1 13.2 - - + +
118A GLY* 4.1 8.7 - - - -
119A ALA* 3.7 29.4 - - + +
122A ILE* 5.1 0.7 - - + -
133A MET* 3.8 29.8 - - + -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASN* 2.8 33.1 + - - +
102A LYS* 4.1 6.9 - - - +
104A LEU* 1.3 74.6 - - - +
106A TYR* 1.3 62.8 + - - +
108A ALA* 3.5 7.3 + - - +
109A SER* 3.0 23.4 + - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 4.3 17.9 - - + -
80A SER* 3.0 29.3 + - - -
82A GLU* 2.7 33.5 + - + -
83A ARG 5.2 3.6 - - - -
84A LEU* 3.7 35.2 - - + -
85A PRO* 6.0 2.9 - - + -
102A LYS 3.1 19.7 + - - +
103A ALA 3.6 4.0 - - - +
104A LEU 3.3 0.2 - - - -
105A ASP* 1.3 77.4 - - - +
107A ILE* 1.3 64.1 + - - +
109A SER* 2.6 27.7 + - - -
110A LYS* 3.2 36.3 + - + +
141A PHE* 3.9 13.5 - + - -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 5.6 0.2 - - + -
76A LEU* 3.9 22.2 - - + -
103A ALA* 3.2 27.3 + - + +
104A LEU* 3.9 20.6 - - + +
105A ASP 3.4 0.2 - - - -
106A TYR* 1.3 73.7 - - + +
108A ALA* 1.3 66.0 + - - +
110A LYS* 3.1 17.1 + - - +
111A GLY 3.5 0.5 + - - -
112A VAL* 3.4 44.4 + - + +
114A LEU* 4.6 9.4 - - + -
133A MET* 5.0 4.0 - - + -
136A THR* 4.6 7.6 - - - +
137A ILE* 3.8 31.0 - - + -
141A PHE* 5.0 8.5 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU 3.0 18.1 + - - +
105A ASP* 3.6 8.7 - - - +
107A ILE* 1.3 74.9 - - - +
109A SER* 1.3 57.8 + - - +
111A GLY* 3.0 21.1 + - - -
112A VAL 3.3 18.1 + - - +
114A LEU* 4.9 5.8 - - + +
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP 3.0 15.4 + - - -
106A TYR* 2.6 28.4 + - - -
108A ALA* 1.3 76.4 - - - +
110A LYS* 1.3 65.4 + - - +
111A GLY 3.3 1.4 + - - -
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 5.9 0.4 - - - -
82A GLU* 3.5 26.5 + - - +
106A TYR* 3.3 46.9 - - + +
107A ILE 3.1 8.5 + - - +
108A ALA 3.1 0.8 - - - -
109A SER* 1.3 85.3 - - - +
111A GLY* 1.3 51.4 + - - -
112A VAL 3.7 1.8 - - - -
140A ARG* 2.6 55.2 + - + +
141A PHE* 4.0 21.1 - - + -
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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