Contacts of the helix formed by residues 99 - 105 (chain B) in PDB entry 1X7W
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 PHE 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.8 3.6 - - + -
54B PHE* 3.7 30.5 - + - -
97B ILE* 3.4 12.0 - - - +
98B GLN* 1.3 97.6 - - + +
100B ALA* 1.3 60.0 + - - +
101B ASP* 3.5 10.8 - - - +
102B TYR* 2.8 50.4 + + + -
134B SER* 3.2 6.3 - - - -
135B PRO* 4.0 4.7 - - - -
139B VAL* 6.3 0.2 - - + -
145B TYR 4.3 0.4 - - - +
146B HIS* 3.6 52.9 - + + -
191B LYS* 3.9 22.2 - - + -
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Residues in contact with ALA 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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99B PHE* 1.3 73.2 - - - +
101B ASP* 1.3 63.3 + - - +
103B ILE* 2.9 29.4 + - - +
104B PHE* 4.6 0.7 - - - -
134B SER* 3.0 9.8 + - - +
135B PRO 2.8 22.9 + - - +
136B TRP* 4.2 6.3 - - - -
148B GLN 4.2 2.7 - - - +
150B PRO* 3.6 31.6 - - + +
188B PHE* 3.6 21.5 - - + -
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Residues in contact with ASP 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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99B PHE* 3.5 14.1 - - + +
100B ALA* 1.3 80.0 + - - +
102B TYR* 1.3 64.5 + - + +
103B ILE 3.3 0.7 - - - -
104B PHE* 3.4 22.8 - - - +
105B PRO* 5.3 0.3 - - - +
145B TYR* 2.9 47.9 - - + +
146B HIS 3.6 10.6 - - - -
147B SER 3.0 1.0 + - - -
148B GLN* 2.8 55.7 + - - +
191B LYS* 4.4 3.1 + - - -
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Residues in contact with TYR 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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46B GLU* 6.0 0.4 - - - -
76B GLU* 3.2 41.5 - - + +
97B ILE* 3.7 5.8 - - + -
98B GLN* 5.0 7.9 - - + +
99B PHE* 2.8 48.3 + + + +
101B ASP* 1.3 79.7 - - + +
103B ILE* 1.3 63.1 + - - +
104B PHE 3.3 2.0 - - - +
105B PRO* 3.2 12.6 - - + +
145B TYR* 3.6 38.5 + + + +
146B HIS* 3.7 14.4 + + - -
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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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97B ILE* 3.8 25.3 - - + +
100B ALA* 2.9 24.0 + - + +
102B TYR* 1.3 79.8 - - - +
104B PHE* 1.3 74.8 + - + +
105B PRO 3.4 0.4 - - - -
106B ALA* 2.9 25.8 + - + +
107B PHE* 3.5 3.8 + - - -
110B ILE* 3.7 21.8 - - + -
132B ILE* 4.4 12.3 - - + -
134B SER* 5.1 2.0 - - - -
150B PRO* 4.5 4.3 - - + -
154B PHE* 3.7 36.6 - - + -
186B ILE* 4.3 11.9 - - + -
188B PHE* 4.3 17.3 - - + -
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Residues in contact with PHE 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 ALA 4.6 0.7 - - - -
101B ASP* 3.4 28.3 - - - +
102B TYR 3.3 0.4 - - - -
103B ILE* 1.3 85.0 - - + +
105B PRO* 1.3 68.0 - - + +
107B PHE* 2.9 37.6 + + + +
148B GLN* 3.3 29.2 - - - -
150B PRO* 3.8 19.7 - - + -
153B PHE* 3.6 43.5 - + + -
154B PHE* 4.8 0.9 - + - -
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Residues in contact with PRO 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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76B GLU* 4.0 23.8 - - + +
77B GLN* 3.4 32.2 + - - +
101B ASP 5.3 0.2 - - - +
102B TYR* 3.2 22.7 - - + +
103B ILE 3.4 0.4 - - - -
104B PHE* 1.3 93.3 - - + +
106B ALA* 1.4 56.6 + - - +
107B PHE 3.6 0.7 + - - -
108B ASP* 4.7 5.0 + - - +
109B GLN 5.5 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