Contacts of the helix formed by residues 92 - 102 (chain J) in PDB entry 6H25
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 GLN 92 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B ASP* 5.3 7.5 + - - -
12B TYR* 5.8 4.8 - - - +
13B ARG 5.6 2.2 + - - -
91J LEU* 1.3 72.1 - - - +
93J THR* 1.3 60.6 + - - +
95J LEU* 3.3 11.5 + - + +
96J GLN* 2.9 36.3 + - + +
122J THR* 5.1 9.2 - - + -
123J PHE 3.1 17.6 + - - +
124J THR* 3.3 32.2 - - + +
125J ASN* 3.5 9.3 + - - +
126J GLU* 4.4 8.2 + - + +
127J HIS* 3.9 25.1 + - - -
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Residues in contact with THR 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU 3.4 0.6 - - - -
92J GLN* 1.3 78.6 - - - +
94J VAL* 1.3 59.0 + - - +
96J GLN* 3.4 7.9 + - - +
97J GLU* 3.0 31.1 + - + +
125J ASN* 3.1 19.2 + - - -
126J GLU* 2.3 37.9 + - - +
144J ARG* 5.4 0.4 - - - +
145J ASN* 3.4 41.7 - - + +
148J ALA* 5.2 4.0 - - + +
149J ILE* 5.0 7.0 - - + -
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Residues in contact with VAL 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J PRO* 4.3 15.5 - - + +
69J ASP 3.9 4.9 - - - +
70J THR* 3.7 32.3 - - + +
73J LEU* 3.7 25.6 - - + -
90J VAL* 5.4 1.1 - - + -
91J LEU* 3.6 26.4 + - + +
92J GLN 3.3 0.2 - - - -
93J THR* 1.3 75.2 - - - +
95J LEU* 1.3 58.1 + - - +
97J GLU* 3.3 3.8 + - - +
98J VAL* 2.9 33.4 + - - +
149J ILE* 3.7 29.4 - - + -
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Residues in contact with LEU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP* 5.4 7.2 - - - +
73J LEU* 5.4 1.8 - - + -
90J VAL* 4.6 9.4 - - + +
91J LEU 3.3 11.6 + - - +
92J GLN* 3.3 13.3 + - + +
94J VAL* 1.3 80.7 - - - +
96J GLN* 1.3 57.1 + - - +
98J VAL* 3.3 6.3 + - + +
99J ARG* 2.9 27.4 + - - +
106J TYR* 3.8 31.4 - - + +
109J ILE* 3.9 32.1 - - + -
110J ARG* 5.3 9.4 - - - +
122J THR* 4.6 20.9 - - + +
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Residues in contact with GLN 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J GLN* 2.9 24.3 + - + +
93J THR* 3.9 7.4 - - - +
95J LEU* 1.3 73.8 - - - +
97J GLU* 1.3 61.5 + - - +
99J ARG* 3.2 16.1 + - + +
100J ASN* 3.0 39.0 + - - +
126J GLU* 5.5 6.1 - - - +
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Residues in contact with GLU 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J THR* 3.1 36.4 + - + +
93J THR* 3.0 18.2 + - + +
94J VAL* 3.7 4.8 - - - +
95J LEU 3.3 0.2 - - - -
96J GLN* 1.3 74.3 - - - +
98J VAL* 1.3 59.9 + - - +
100J ASN* 3.2 10.6 + - + +
101J ARG* 2.9 51.5 + - + +
142J ASN* 4.3 17.7 + - - +
145J ASN* 4.5 25.0 + - - +
146J ASN* 6.0 0.2 + - - -
149J ILE* 5.5 1.2 - - - +
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Residues in contact with VAL 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J THR* 4.6 4.9 - - + -
73J LEU* 4.0 24.2 - - + -
74J LEU* 3.8 27.1 - - + -
94J VAL* 2.9 23.3 + - + +
95J LEU* 3.6 7.4 - - + +
97J GLU* 1.3 76.8 - - - +
99J ARG* 1.3 56.5 + - - +
101J ARG* 4.3 0.7 - - - +
102J SER 2.9 36.5 + - - +
105J VAL* 3.9 15.3 - - + -
106J TYR* 3.8 29.2 - - + +
109J ILE* 4.0 9.0 - - + -
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Residues in contact with ARG 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.2 45.0 - - - +
95J LEU 2.9 14.3 + - - +
96J GLN* 3.2 19.2 + - + +
98J VAL* 1.3 77.1 - - - +
100J ASN* 1.3 66.4 + - - +
102J SER 4.7 4.6 + - - +
103J ALA* 5.4 0.6 + - - +
106J TYR* 4.0 46.9 + - + -
365J ILE* 4.3 33.4 - - + +
367J GLU* 4.6 7.7 + - - +
368J SER* 6.1 0.2 - - - +
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Residues in contact with ASN 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J GLN* 3.0 30.0 + - - +
97J GLU* 3.6 11.6 - - + +
98J VAL 3.2 0.2 - - - -
99J ARG* 1.3 85.7 + - - +
101J ARG* 1.3 66.4 + - + +
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Residues in contact with ARG 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J THR* 5.6 0.6 - - - +
71J ASN* 4.6 10.1 + - - -
74J LEU* 3.9 38.0 - - + +
75J HIS* 5.8 3.4 + - - -
97J GLU* 2.9 39.5 + - + +
98J VAL 3.0 2.0 + - - +
100J ASN* 1.3 83.4 - - + +
102J SER* 1.3 62.6 + - - +
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Residues in contact with SER 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74J LEU* 4.4 9.9 - - - -
98J VAL 2.9 19.7 + - - +
99J ARG* 4.8 2.9 - - - -
100J ASN 3.8 0.2 - - - -
101J ARG* 1.3 75.6 - - - +
103J ALA* 1.3 66.0 + - - +
104J PRO* 3.4 11.3 - - - +
105J VAL* 3.4 29.6 - - - +
106J TYR* 3.5 14.6 + - - +
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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