Contacts of the helix formed by residues 102 - 107 (chain A) in PDB entry 5JQE
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 TYR 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LEU* 1.3 76.8 - - - +
103A PRO* 1.3 78.2 - - + +
104A PHE* 3.4 19.5 - + + -
105A THR* 2.9 21.7 + - + -
106A TRP* 4.0 3.8 - - - -
122A VAL* 6.3 0.2 - - + -
314A VAL 3.9 3.4 - - - -
315A ALA* 3.2 27.7 + - - +
317A LYS* 3.5 32.9 + - + +
320A GLU* 3.1 44.8 - - + +
321A GLU* 4.3 9.2 + - - +
333A MET* 3.5 26.5 - - + +
337A GLN* 4.3 11.0 - - - -
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Residues in contact with PRO 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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101A LEU 3.7 2.4 - - - +
102A TYR* 1.3 94.2 - - + +
104A PHE* 1.3 70.2 + - + +
105A THR 3.2 1.0 + - - -
106A TRP* 3.4 21.7 + - + +
107A ASP* 4.3 4.9 - - - +
110A ARG* 5.5 0.9 + - - -
317A LYS* 4.5 7.2 - - - +
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Residues in contact with PHE 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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102A TYR* 3.9 12.6 - - + -
103A PRO* 1.3 86.3 - - + +
105A THR* 1.3 77.8 + - + +
107A ASP* 2.9 32.8 + - - +
122A VAL* 4.3 15.7 - - + -
271A VAL* 4.5 5.6 - - + -
273A VAL* 5.6 0.7 - - + -
333A MET* 3.7 36.6 - - + -
336A ALA* 4.3 17.3 - - + -
337A GLN* 3.7 27.4 - - + +
341A ILE* 3.1 35.1 - - + +
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Residues in contact with THR 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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101A LEU* 4.0 10.7 - - - +
102A TYR* 2.9 21.8 + - + +
104A PHE* 1.3 104.0 - - + +
106A TRP* 1.3 61.3 + - - +
107A ASP 3.4 0.2 - - - -
108A ALA* 3.7 15.7 + - - +
109A VAL* 4.1 2.8 - - - +
119A PRO* 3.2 36.1 - - + +
122A VAL* 3.8 20.6 - - + -
273A VAL* 4.8 5.3 - - + +
315A ALA* 3.9 12.1 - - + -
341A ILE* 4.6 3.4 - - - -
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Residues in contact with TRP 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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91A ILE* 4.3 9.0 - - + -
93A PRO* 4.3 7.9 - - + -
97A PHE* 3.8 20.2 - + - -
98A GLN* 3.0 51.0 + - + +
101A LEU* 3.5 29.3 - - + +
102A TYR 4.0 10.1 + - - -
103A PRO* 3.4 15.9 + - + +
104A PHE 3.0 1.6 + - - -
105A THR* 1.3 73.5 + - - +
107A ASP* 1.3 64.2 + - - +
108A ALA 3.1 3.0 + - - -
109A VAL* 3.4 19.6 + - + +
110A ARG* 3.1 31.8 + - - +
115A LEU* 3.5 28.4 - - + +
117A ALA 4.0 7.9 - - - -
118A TYR* 4.5 3.4 - + - -
119A PRO* 3.5 29.8 - - + -
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Residues in contact with ASP 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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103A PRO 4.3 2.6 - - - +
104A PHE* 2.9 29.3 + - - +
106A TRP* 1.3 77.5 - - - +
108A ALA* 1.3 57.5 + - - +
109A VAL 3.4 0.2 - - - -
110A ARG* 3.3 26.0 + - - +
183A TYR* 3.4 49.9 + - + -
188A TYR* 5.3 4.9 + - - -
341A ILE* 4.2 13.4 - - + +
344A ASN* 5.3 1.6 + - - -
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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