Contacts of the helix formed by residues 94 - 105 (chain D) in PDB entry 6N1G
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 ASN 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D HIS 2.8 9.1 + - - +
93D MET* 1.3 80.2 - - - +
95D ALA* 1.3 64.8 + - - +
96D ALA* 3.0 10.3 + - - +
97D VAL* 3.5 27.8 - - + +
98D THR* 3.0 23.6 + - - -
119D GLN* 3.2 8.6 - - - +
179D THR* 5.1 1.6 - - - +
182D LEU* 4.4 2.0 - - - +
225D ILE* 3.5 32.7 + - - +
226D ASN* 2.9 23.7 - - - +
227D PRO* 3.1 17.0 - - - +
403D GOL 4.8 1.1 - - - +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 1.3 74.1 + - - +
96D ALA* 1.3 56.9 + - - +
98D THR* 4.1 2.7 - - - -
99D PHE* 3.4 23.7 + - - +
112D PHE* 3.6 10.5 - - + -
116D VAL* 3.5 28.7 - - + -
119D GLN* 3.3 12.3 + - - +
226D ASN* 3.4 5.4 + - - +
227D PRO* 3.9 24.5 - - + -
228D SER* 4.9 4.7 - - - +
262D LEU* 4.9 5.5 - - + +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 3.0 13.8 + - - +
95D ALA* 1.3 77.4 - - - +
97D VAL* 1.3 60.1 + - - +
98D THR 3.2 1.8 - - - -
99D PHE* 3.4 5.9 + - - +
100D ALA* 2.9 30.1 + - - +
179D THR* 4.5 2.9 - - + -
227D PRO* 4.0 6.2 - - + +
261D PRO* 3.6 33.7 - - + +
262D LEU* 3.9 8.9 - - - +
265D ALA* 3.6 12.6 - - + +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 3.2 41.5 + - + +
94D ASN* 3.2 30.7 + - + +
96D ALA* 1.3 76.2 - - + +
98D THR* 1.3 62.0 + - - +
100D ALA* 3.9 0.8 - - - +
101D ASN* 3.1 28.1 + - - +
179D THR* 6.1 0.4 - - + -
182D LEU* 4.1 8.3 - - + -
183D GLN* 3.4 26.3 + - - +
186D LEU* 3.9 25.4 - - + -
187D PHE* 5.5 0.2 - - - -
265D ALA* 5.4 0.9 - - + -
403D GOL 4.2 6.1 - - - +
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Residues in contact with THR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 2.8 40.8 + - + +
94D ASN 3.0 16.7 + - - -
95D ALA* 4.1 2.9 - - - -
97D VAL* 1.3 75.5 - - - +
99D PHE* 1.3 60.8 + - - +
101D ASN* 3.3 1.6 + - - +
102D CYS* 2.8 40.2 + - - -
107D VAL* 4.9 0.9 - - + -
112D PHE* 3.4 28.0 - - + +
115D TYR* 4.0 18.6 - - + -
116D VAL* 6.4 0.9 - - - -
119D GLN* 3.6 7.6 + - - -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ALA 3.4 9.9 + - - +
96D ALA* 3.4 6.1 + - - +
98D THR* 1.3 79.7 - - - +
100D ALA* 1.3 58.1 + - + +
102D CYS* 4.0 6.2 + - + +
103D ALA* 3.5 25.9 + - + +
112D PHE* 3.3 40.3 - + + -
262D LEU* 3.9 41.7 - - + -
266D TYR* 5.4 14.6 - + + -
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA 2.9 11.3 + - - +
97D VAL 4.3 0.2 - - - +
99D PHE* 1.3 75.8 - - - +
101D ASN* 1.3 61.7 + - - +
102D CYS 3.3 1.6 - - - -
103D ALA* 3.9 5.1 - - - +
104D LEU* 3.0 31.4 + - + +
183D GLN* 3.3 30.1 - - + +
187D PHE* 4.3 7.1 - - + -
265D ALA 3.7 22.0 - - - +
266D TYR* 4.5 7.0 - - + +
269D GLY* 5.4 1.1 - - - -
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Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D HIS* 3.8 17.6 + - + -
97D VAL 3.1 20.4 + - - +
98D THR* 3.3 4.5 + - - +
100D ALA* 1.3 76.3 - - - +
102D CYS* 1.3 56.0 + - - +
105D GLY* 2.8 46.0 + - - +
106D ARG 3.2 0.2 + - - -
107D VAL* 3.1 27.4 + - + +
187D PHE* 4.7 15.4 - - + -
401D GOL 5.3 4.0 - - - -
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Residues in contact with CYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR* 2.8 33.9 + - - +
99D PHE* 4.1 8.1 - - + +
101D ASN* 1.3 78.8 - - - +
103D ALA* 1.3 59.7 + - - +
106D ARG* 4.0 10.4 + - - -
107D VAL* 3.3 43.1 + - - +
108D PRO 4.3 2.2 - - - -
109D TRP* 5.0 5.8 - - + -
112D PHE* 3.9 26.7 - - + -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D PHE* 3.5 22.3 + - + +
100D ALA 3.7 3.1 + - - +
101D ASN 3.5 0.2 - - - -
102D CYS* 1.3 79.2 - - - +
104D LEU* 1.3 60.0 + - + +
105D GLY 3.9 0.2 - - - -
106D ARG 5.3 0.4 - - - -
266D TYR* 4.0 30.8 - - + -
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Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA 3.0 16.2 + - - +
101D ASN* 4.8 0.4 - - - -
103D ALA* 1.3 78.4 - - + +
105D GLY* 1.3 59.0 + - - +
106D ARG 3.8 1.1 - - - -
187D PHE* 3.8 12.3 - - + -
266D TYR* 6.3 2.2 - - + -
269D GLY* 3.1 38.4 - - - +
270D ILE* 4.3 13.5 - - + -
273D LEU* 3.9 31.9 - - + +
401D GOL 3.1 39.5 - - - +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASN* 2.8 34.0 + - - +
104D LEU* 1.3 79.0 - - - +
106D ARG* 1.3 90.4 + - - +
107D VAL* 3.1 4.5 + - - +
401D GOL 4.8 9.4 - - - -
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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