Contacts of the helix formed by residues 98 - 107 (chain B) in PDB entry 3T06
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 LYS 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP* 4.7 4.2 + - - +
64B GLU* 2.9 27.3 + - - +
65B ASP* 5.3 1.6 + - - -
67B ASP* 4.9 2.5 + - - -
70B ARG* 3.8 22.8 - - - +
94B ASN* 2.8 30.7 + - - +
97B GLU* 1.3 77.7 - - + +
99B TRP* 1.3 97.1 + - + +
100B THR 3.7 0.9 - - - -
101B PRO* 3.6 7.9 - - - +
102B GLU* 3.5 20.6 + - - +
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.8 26.7 - - + -
12B GLY* 3.2 37.2 - - - -
13B ASP* 2.9 29.0 + - - +
18B LYS* 5.2 0.9 - - - -
60B THR* 5.5 2.9 - - - -
64B GLU* 4.1 18.2 - - + -
70B ARG* 3.5 35.7 - - - -
74B TYR* 3.9 2.7 - - - -
82B MET* 4.0 21.8 - - + -
94B ASN* 3.1 21.1 + - + -
95B ILE* 4.1 9.9 - - + +
98B LYS* 1.3 105.6 - - + +
100B THR* 1.3 62.1 + - - +
102B GLU* 3.5 14.2 + - - +
103B VAL* 2.9 32.3 + - + +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B MET* 3.4 30.1 - - + -
95B ILE* 3.0 17.5 + - + +
96B PRO* 4.0 6.2 + - - +
99B TRP* 1.3 71.8 - - - +
101B PRO* 1.3 83.3 - - - +
103B VAL* 2.9 1.6 + - - -
104B LYS* 2.8 42.2 + - - +
112B ILE* 5.7 2.0 - - - -
151B ILE* 3.7 35.9 - - + +
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A THR* 4.9 8.1 - - - +
1065A SER* 3.6 28.5 - - - +
1066A ASP* 5.7 4.7 - - + +
95B ILE 4.0 0.2 - - - +
96B PRO 3.4 15.7 - - - +
97B GLU 3.9 0.7 - - - +
98B LYS 3.6 15.0 - - - +
100B THR* 1.3 98.2 - - - +
102B GLU* 1.3 62.1 + - - +
104B LYS* 3.7 5.7 + - + +
105B HIS* 3.2 22.9 + - - +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASP 5.4 1.1 - - - +
70B ARG* 2.9 40.8 + - - -
71B PRO* 5.6 1.1 - - - -
74B TYR* 2.5 40.5 + - + +
98B LYS* 3.5 19.7 - - - +
99B TRP* 3.5 12.4 + - - +
100B THR 3.1 0.6 - - - -
101B PRO* 1.3 82.8 - - - +
103B VAL* 1.3 59.3 + - - +
105B HIS* 2.9 21.4 + - - +
106B PHE* 3.1 28.6 + - + -
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.3 14.1 - - + -
74B TYR* 4.2 25.6 - - + +
80B ILE* 3.8 32.5 - - + -
82B MET* 4.0 13.9 - - + -
99B TRP* 2.9 20.3 + - + +
100B THR* 2.9 6.6 + - - +
102B GLU* 1.3 76.8 - - + +
104B LYS* 1.3 57.0 + - - +
106B PHE 4.7 0.2 - - - +
107B CYS* 2.8 43.2 + - + +
110B VAL 5.5 0.7 - - - +
112B ILE* 4.1 20.2 - - + -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 2.8 30.6 + - - +
101B PRO* 4.2 4.9 - - + +
103B VAL* 1.3 73.7 - - - +
105B HIS* 1.3 62.2 + - - +
107B CYS 4.1 6.7 - - - +
108B PRO* 3.7 17.2 - - - +
109B ASN 6.0 2.7 - - - +
110B VAL 6.1 0.2 - - - +
112B ILE* 4.2 21.3 - - + -
151B ILE* 2.6 35.2 + - - +
152B GLY* 4.7 3.6 - - - -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A GLU* 5.8 2.5 + - - -
971A PRO* 5.7 9.5 - - + +
1062A LEU* 6.3 2.5 - - + -
101B PRO 3.2 13.7 + - - +
102B GLU* 2.9 12.0 + - - +
104B LYS* 1.3 80.8 - - - +
106B PHE* 1.3 91.3 + + + +
108B PRO* 3.7 7.4 - - - +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A ARG* 6.4 0.2 - - - -
67B ASP 5.5 0.4 - - - -
68B ARG* 6.1 3.1 - - - -
71B PRO* 3.8 35.7 - - + -
74B TYR* 3.6 40.6 - + + +
75B PRO* 5.3 1.9 - - - +
102B GLU* 3.1 39.2 + - + +
105B HIS* 1.3 102.2 - + + +
107B CYS* 1.3 64.2 + - - +
108B PRO* 3.3 8.5 - - - +
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Residues in contact with CYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B TYR* 3.8 41.7 - - - -
77B THR* 4.5 5.2 - - - -
80B ILE* 4.5 12.8 - - + -
103B VAL* 2.8 28.3 + - + +
104B LYS* 4.0 7.0 - - - +
106B PHE* 1.3 87.9 - - - +
108B PRO* 1.3 68.3 - - - +
109B ASN 3.3 1.2 + - - -
110B VAL* 3.2 32.6 + - + +
112B ILE* 5.9 0.2 - - - +
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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