Contacts of the helix formed by residues 101 - 106 (chain B) in PDB entry 1Q6X
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 ALA 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ARG 3.7 1.0 + - - -
100B LEU* 1.3 75.1 - - - +
102B LEU* 1.3 65.4 + - - +
103B PRO* 3.8 4.0 - - + -
105B ASN* 3.1 26.9 + - - +
106B SER* 4.9 0.3 - - - -
247B SER 3.1 26.9 - - - +
248B ASP* 3.6 20.9 - - - +
249B GLY* 4.0 4.7 - - - +
250B ARG* 4.8 0.4 - - - +
393B LYS* 6.6 0.2 - - + -
397B ILE* 4.0 19.7 - - + -
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Residues in contact with LEU 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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100B LEU 3.5 2.6 + - - +
101B ALA* 1.3 71.9 - - - +
103B PRO* 1.3 72.4 - - + +
106B SER* 2.9 21.6 + - - +
107B SER* 2.9 36.0 + - - +
173B ARG* 3.6 36.6 - - - +
246B THR 5.3 0.2 + - - -
248B ASP 4.6 1.2 + - - -
250B ARG* 3.2 41.4 - - - +
314B TYR* 3.5 37.2 - - + +
315B ASP* 4.1 1.6 - - - +
333B GLU* 4.2 12.8 - - + +
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Residues in contact with PRO 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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101B ALA* 3.3 11.0 - - + +
102B LEU* 1.3 93.2 - - + +
104B VAL* 1.3 63.9 + - + +
105B ASN* 2.7 20.8 + - - -
107B SER* 4.9 2.0 - - - -
247B SER* 3.7 28.9 - - - +
300B LEU 4.2 7.0 - - - +
301B HIS* 4.9 1.6 - - + -
314B TYR* 3.5 47.1 - - + +
394B LEU* 4.8 8.7 - - + -
397B ILE* 4.1 12.5 - - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 3.3 2.0 + - - -
103B PRO* 1.3 72.7 - - - +
105B ASN* 1.3 64.2 + - - +
106B SER* 3.4 2.5 - - - -
107B SER 4.3 11.3 + - - +
300B LEU* 4.1 23.7 + - + +
301B HIS* 4.2 20.0 - - + -
397B ILE* 3.5 26.9 - - + -
401B LEU* 4.1 31.6 - - + -
562B TYR* 4.8 1.2 - - - +
563B GLY* 3.1 39.1 + - - +
564B PRO* 4.9 0.2 - - + -
588B PHE* 4.5 17.7 - - + -
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Residues in contact with ASN 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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98B ASN* 5.3 5.8 + - - +
100B LEU* 3.7 38.8 - - + +
101B ALA* 3.1 31.1 + - - +
103B PRO 2.7 17.1 + - - -
104B VAL* 1.3 75.8 - - - +
106B SER* 1.3 59.4 + - - +
397B ILE* 4.4 9.7 - - - +
563B GLY 4.9 2.4 - - - +
564B PRO 4.3 16.3 - - - +
565B VAL* 4.7 10.9 - - - +
588B PHE* 3.8 24.3 - - - -
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Residues in contact with SER 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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95B TYR* 3.9 25.7 - - - -
98B ASN* 5.3 10.3 - - - -
100B LEU 5.8 0.4 - - - -
101B ALA 4.9 0.4 - - - -
102B LEU* 2.9 33.3 + - - +
104B VAL 3.4 1.3 - - - -
105B ASN* 1.3 81.9 - - - +
107B SER* 1.3 58.9 + - - -
108B PRO* 3.0 15.2 - - - +
173B ARG* 4.3 4.7 + - - -
333B GLU* 4.7 1.7 + - - -
334B HIS* 3.9 15.0 - - - +
562B TYR* 5.3 4.2 - - - +
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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