Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 4I6J
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 HIS 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ALA 3.4 4.7 + - - -
94B THR* 1.3 75.6 - - - +
96B PRO* 1.3 82.0 - - + +
97B GLU* 2.9 39.2 + - + +
98B LEU* 3.0 14.1 + - + +
99B ILE* 3.1 12.3 + - - +
158C GLN* 4.2 11.8 + - + +
159C TRP* 3.1 60.0 + + - +
161C GLU 4.0 10.7 + - - +
162C GLU* 4.7 5.6 - - - +
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Residues in contact with PRO 96 (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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94B THR 3.4 3.8 - - - +
95B HIS* 1.3 103.7 - - + +
97B GLU* 1.3 67.7 + - + +
99B ILE* 3.3 16.6 + - + +
100B LYS* 3.3 26.1 + - - +
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Residues in contact with GLU 97 (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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95B HIS* 2.9 20.2 + - + +
96B PRO* 1.3 83.3 - - + +
98B LEU* 1.3 62.9 + - - +
100B LYS* 3.1 43.1 + - - +
101B GLN* 3.1 21.8 + - - +
159C TRP* 3.2 46.0 - - + +
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Residues in contact with LEU 98 (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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53B LEU* 5.1 4.7 - - + -
70B PHE* 6.4 0.2 - - + -
76B TRP* 4.5 7.6 - - + -
79B PHE* 3.3 37.9 - - + -
94B THR* 3.6 14.6 - - + -
95B HIS* 3.0 12.0 + - + +
97B GLU* 1.3 79.1 - - - +
99B ILE* 1.3 55.5 + - - +
101B GLN* 3.3 20.3 + - - +
102B ILE* 2.9 53.6 + - + +
159C TRP* 3.6 32.6 - - + +
160C CYS* 4.8 13.9 - - - -
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Residues in contact with ILE 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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81B PHE* 4.3 12.8 - - + -
83B LEU* 4.4 13.0 - - + -
94B THR* 3.8 31.4 - - + +
95B HIS 3.1 14.4 + - - +
96B PRO* 3.4 14.4 - - + +
98B LEU* 1.3 76.9 - - - +
100B LYS* 1.3 64.2 + - + +
102B ILE* 3.5 7.5 + - - +
103B ILE* 3.2 30.4 + - + +
130B ILE* 3.7 38.8 - - + -
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Residues in contact with LYS 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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96B PRO* 3.3 10.5 + - - +
97B GLU* 3.1 46.3 + - - +
99B ILE* 1.3 80.0 - - + +
101B GLN* 1.3 57.9 + - - +
103B ILE* 3.3 8.3 + - + +
104B LYS* 2.8 31.4 + - - +
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Residues in contact with GLN 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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70B PHE* 5.1 2.9 - - - -
71B HIS* 3.7 23.8 + - + -
76B TRP* 5.7 0.2 - - - -
97B GLU 3.1 11.7 + - - +
98B LEU* 3.6 24.4 - - + +
100B LYS* 1.3 79.8 - - - +
102B ILE* 1.3 58.3 + - + +
104B LYS* 4.4 5.2 - - - +
105B ARG* 2.8 64.7 + - + +
106B HIS* 5.6 0.7 - - - +
156C GLU* 4.1 13.5 + - - +
159C TRP* 3.5 29.7 - - + -
160C CYS* 5.9 1.2 - - - -
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Residues in contact with ILE 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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76B TRP* 3.1 42.0 - - + -
79B PHE* 4.6 7.9 - - + -
81B PHE* 4.2 19.1 - - + -
98B LEU* 2.9 57.9 + - + +
99B ILE* 3.8 6.7 - - - +
101B GLN* 1.3 72.1 - - + +
103B ILE* 1.3 58.5 + - + +
106B HIS* 2.6 45.6 + - + -
107B SER 3.4 1.7 + - - -
110B LEU* 3.7 30.1 - - + -
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Residues in contact with ILE 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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81B PHE* 5.4 3.4 - - + -
99B ILE* 3.2 32.1 + - + +
100B LYS* 3.7 6.1 - - - +
102B ILE* 1.3 83.5 - - + +
104B LYS* 1.3 61.7 + - - +
107B SER* 3.3 28.5 + - - +
110B LEU* 6.1 0.2 - - - -
130B ILE* 4.2 19.3 - - + -
133B GLN* 3.8 54.1 - - + +
134B LEU* 4.7 14.1 - - + -
136B ASN* 5.8 0.2 + - - -
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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 LYS 2.8 21.6 + - - +
101B GLN* 4.0 5.2 - - - +
103B ILE* 1.3 78.2 - - - +
105B ARG* 1.3 69.3 + - + +
107B SER* 4.8 3.2 + - - -
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Residues in contact with ARG 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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71B HIS* 3.0 49.1 + - - +
101B GLN* 2.8 44.8 + - + +
104B LYS* 1.3 88.0 - - + +
106B HIS* 1.3 85.2 + - + +
107B SER 3.8 1.1 - - - -
108B ASN* 4.1 4.5 - - - +
109B HIS* 3.4 12.8 - - - -
156C GLU* 4.5 10.3 + - - -
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Residues in contact with HIS 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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71B HIS* 3.2 54.2 + + + -
76B TRP* 3.3 54.3 + + + -
101B GLN 4.5 0.9 - - - -
102B ILE* 2.6 35.0 + - + +
105B ARG* 1.3 97.7 + - + +
107B SER* 1.3 64.2 + - - +
108B ASN 3.0 3.6 - - - +
109B HIS* 3.0 20.5 + + - +
110B LEU* 3.0 28.4 + - + +
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Residues in contact with SER 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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102B ILE 3.4 4.3 + - - -
103B ILE* 3.3 25.8 + - - +
104B LYS 4.8 3.5 + - - -
105B ARG 3.8 0.8 - - - -
106B HIS* 1.3 78.1 + - - +
108B ASN* 1.3 65.9 + - - +
109B HIS 3.5 0.2 - - - -
110B LEU* 4.1 7.3 + - - +
133B GLN 5.4 4.7 - - - -
134B LEU* 5.5 2.9 - - - -
136B ASN* 3.8 30.1 + - - +
137B CYS* 3.1 42.3 - - - -
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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