Contacts of the helix formed by residues 90 - 110 (chain A) in PDB entry 4K06
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 5.5 1.9 + - - +
67A CYS* 5.2 0.9 - - - +
87A GLU* 3.5 3.9 + - - +
88A ASN* 1.3 74.8 - - - +
91A PRO* 1.3 69.4 - - - +
92A CYS* 3.4 9.9 + - - +
93A LEU* 3.1 47.9 + - + +
94A LYS* 2.8 33.6 + - - +
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Residues in contact with PRO 91 (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 ASN 3.1 9.2 - - - +
90A ASN* 1.3 92.5 - - - +
92A CYS* 1.3 57.5 + - - +
94A LYS* 3.4 5.7 + - + +
95A GLU* 2.8 44.8 + - + +
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Residues in contact with CYS 92 (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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59A LEU* 3.7 9.0 - - - +
60A THR 3.3 34.3 - - - +
61A GLY* 4.3 2.9 - - - -
67A CYS* 2.0 56.1 - - + +
90A ASN* 3.4 9.9 + - - +
91A PRO* 1.3 79.2 - - - +
93A LEU* 1.3 54.7 + - - +
95A GLU* 3.4 8.7 + - - +
96A LEU* 2.7 35.7 + - - +
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Residues in contact with LEU 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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67A CYS* 3.5 29.2 - - + -
72A ASP* 4.4 12.8 - - + +
73A ARG 4.0 13.9 - - - +
74A TYR* 3.7 20.2 - - + -
87A GLU* 4.0 26.2 - - + +
90A ASN* 3.1 26.0 + - + +
92A CYS* 1.3 76.0 - - - +
94A LYS* 1.3 53.3 + - - +
96A LEU* 3.3 13.9 + - + +
97A CYS* 2.8 34.1 + - - +
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Residues in contact with LYS 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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85A CYS* 4.4 17.9 + - + +
87A GLU* 3.2 33.1 - - - +
88A ASN 4.5 1.6 - - - +
90A ASN 2.8 14.7 + - - +
91A PRO* 3.6 7.0 - - + +
93A LEU* 1.3 74.2 - - - +
95A GLU* 1.3 68.5 + - + +
97A CYS* 3.4 6.0 + - - +
98A GLU* 2.9 58.8 + - + +
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Residues in contact with GLU 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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52A CYS* 4.7 0.2 - - - -
58A LYS* 4.7 21.6 - - - +
59A LEU* 3.5 22.7 - - + +
91A PRO* 2.8 31.6 + - + +
92A CYS* 3.7 2.5 + - - +
94A LYS* 1.3 77.6 - - + +
96A LEU* 1.3 62.1 + - - +
98A GLU* 3.1 8.8 + - - +
99A CYS* 2.8 32.4 + - - -
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Residues in contact with LEU 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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53A TYR* 3.5 29.4 - - + +
59A LEU* 3.5 19.2 - - + +
67A CYS* 4.0 14.1 - - - -
68A ASP 4.0 8.3 - - - +
69A PRO* 3.6 28.7 - - + +
72A ASP 4.3 3.4 - - - +
74A TYR* 3.8 25.8 - - + -
92A CYS 2.7 22.0 + - - +
93A LEU* 3.4 11.7 - - + +
95A GLU* 1.3 73.1 - - - +
97A CYS* 1.3 62.8 + - - +
99A CYS* 3.1 6.5 + - - +
100A ASP* 3.1 26.2 + - - +
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Residues in contact with CYS 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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8A MET* 3.6 10.6 - - - +
74A TYR* 3.5 34.8 - - + -
75A SER 4.5 1.3 - - - +
76A TYR* 3.9 5.8 - - - -
85A CYS* 2.0 54.5 - - + -
87A GLU* 5.4 1.3 - - + -
93A LEU 2.8 21.4 + - - +
94A LYS* 3.5 5.2 - - - +
96A LEU* 1.3 74.4 - - - +
98A GLU* 1.3 54.8 + - - +
100A ASP* 3.2 3.6 + - - +
101A LYS* 2.8 29.1 + - - +
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Residues in contact with GLU 98 (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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52A CYS* 5.1 0.7 - - - -
85A CYS* 3.3 21.0 + - - +
94A LYS* 2.9 51.8 + - - +
95A GLU* 3.1 9.8 + - - +
97A CYS* 1.3 73.4 - - - +
99A CYS* 1.3 60.4 + - - +
101A LYS* 3.8 22.3 + - - +
102A ALA* 3.0 28.4 + - - +
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Residues in contact with CYS 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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49A HIS* 3.2 11.8 - - + -
52A CYS* 2.0 66.0 - - + -
53A TYR* 3.9 17.0 - - + -
58A LYS* 5.6 0.2 - - - -
59A LEU* 4.3 7.9 - - - -
95A GLU* 2.8 25.2 + - - -
96A LEU* 3.1 8.9 + - - +
98A GLU* 1.3 75.9 - - - +
100A ASP* 1.3 62.6 + - - +
102A ALA* 3.2 6.3 + - - +
103A VAL 3.2 18.2 + - - -
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Residues in contact with ASP 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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1A SER 4.2 2.6 + - - +
5A LEU* 3.8 23.9 + - + +
8A MET* 3.5 10.5 - - - +
49A HIS* 2.6 21.4 + - - -
53A TYR* 2.6 33.5 + - - -
74A TYR* 2.5 39.9 + - - +
96A LEU* 3.1 9.9 + - - +
97A CYS 3.7 1.3 - - - +
99A CYS* 1.3 72.8 - - - +
101A LYS* 1.3 65.5 + - - +
103A VAL* 3.3 5.0 - - - +
104A ALA* 3.2 24.4 + - - +
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Residues in contact with LYS 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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8A MET* 3.4 8.6 - - - -
82A THR* 4.1 9.9 - - - +
83A ILE* 2.7 55.4 + - + +
84A VAL* 4.9 2.0 - - - +
85A CYS* 4.5 3.3 - - - +
97A CYS 2.8 16.8 + - - +
98A GLU* 3.8 28.2 + - - +
100A ASP* 1.3 77.1 - - - +
102A ALA* 1.3 62.8 + - - +
104A ALA* 3.5 1.7 + - - +
105A ILE* 3.1 45.8 + - + +
202A SO4 4.1 7.2 + - - -
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Residues in contact with ALA 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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48A VAL* 6.0 6.1 - - + -
52A CYS* 6.0 1.3 - - - -
98A GLU 3.0 18.1 + - - +
99A CYS* 3.2 7.6 + - - +
101A LYS* 1.3 79.3 - - - +
103A VAL* 1.3 58.0 + - - +
105A ILE* 3.3 8.3 + - - +
106A CYS* 2.8 30.6 + - - +
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Residues in contact with VAL 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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5A LEU* 3.6 18.8 - - + -
9A ILE* 4.9 4.0 - - + -
45A CYS* 3.5 33.9 - - + +
46A CYS* 3.9 8.7 - - - +
49A HIS* 3.4 38.8 - - + +
99A CYS 3.2 2.0 + - - -
100A ASP 3.3 12.1 - - - +
102A ALA* 1.3 78.0 - - - +
104A ALA* 1.3 57.7 + - + +
106A CYS* 3.2 5.0 + - - +
107A LEU* 2.7 50.7 + - + +
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Residues in contact with ALA 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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8A MET* 3.7 37.5 - - + +
9A ILE* 3.8 15.0 - - + +
12A GLU* 3.2 23.4 - - + +
13A THR* 4.2 0.9 - - - +
83A ILE* 4.5 0.7 - - + -
100A ASP 3.2 14.3 + - - +
101A LYS 3.9 3.6 - - - +
102A ALA 3.3 0.2 - - - -
103A VAL* 1.3 82.1 - - - +
105A ILE* 1.3 62.5 + - - +
107A LEU* 3.5 4.1 + - - +
108A ARG 3.2 14.4 + - - -
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Residues in contact with ILE 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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12A GLU* 3.9 24.5 - - - +
101A LYS* 3.1 40.3 + - + +
102A ALA* 3.6 6.5 - - - +
104A ALA* 1.3 75.6 - - - +
106A CYS* 1.3 65.0 + - - +
108A ARG* 3.3 18.5 + - - +
109A GLU* 3.0 41.3 + - - +
202A SO4 3.3 29.2 - - - +
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Residues in contact with CYS 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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41A ALA 4.6 0.4 - - - -
45A CYS* 2.0 52.2 - - + -
48A VAL* 6.2 1.6 - - - -
102A ALA 2.8 17.5 + - - +
103A VAL* 3.4 6.3 - - - +
105A ILE* 1.3 78.9 - - - +
107A LEU* 1.3 60.1 + - - +
109A GLU* 3.4 12.7 + - - +
110A ASN* 2.8 38.6 + - - -
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Residues in contact with LEU 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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9A ILE* 3.9 28.5 - - + -
13A THR* 3.8 14.1 - - + -
23A TYR* 3.7 35.5 + - + -
42A THR* 3.5 44.0 + - + +
45A CYS* 3.8 8.7 - - + -
46A CYS* 4.3 9.2 - - - -
103A VAL* 2.7 36.7 + - + +
104A ALA* 3.8 1.6 - - - +
105A ILE 3.3 0.4 - - - -
106A CYS* 1.3 71.6 - - - +
108A ARG* 1.3 59.0 + - - +
110A ASN* 3.4 3.5 + - - +
111A LEU* 3.0 30.3 + - - +
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Residues in contact with ARG 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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12A GLU* 2.6 56.7 + - - +
13A THR* 3.8 7.1 - - - +
104A ALA 3.2 10.5 + - - +
105A ILE* 3.6 22.6 - - - +
107A LEU* 1.3 78.0 - - - +
109A GLU* 1.3 77.2 + - - +
110A ASN 3.2 1.0 + - - -
111A LEU* 3.2 22.9 + - + +
202A SO4 3.1 31.9 + - - -
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Residues in contact with GLU 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 ILE* 3.0 35.6 + - - +
106A CYS* 3.7 14.4 - - - +
107A LEU 3.3 0.2 - - - -
108A ARG* 1.3 93.4 + - - +
110A ASN* 1.3 67.3 + - - +
111A LEU 3.9 0.2 + - - -
112A GLY 4.8 2.1 + - - -
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Residues in contact with ASN 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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41A ALA* 3.2 33.6 + - + +
42A THR* 3.4 21.4 + - - +
45A CYS* 3.5 14.3 - - - -
106A CYS* 2.8 32.2 + - - +
107A LEU 3.5 3.4 - - - +
108A ARG 3.1 0.6 - - - -
109A GLU* 1.3 85.7 + - - +
111A LEU* 1.3 63.3 + - - +
112A GLY 3.0 4.5 + - - +
113A THR* 3.2 18.2 + - - +
114A TYR 3.5 1.2 + - - -
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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