Contacts of the helix formed by residues 94 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A HIS 2.9 9.1 + - - +
93A MET* 1.3 81.0 - - - +
95A ALA* 1.3 63.0 + - - +
96A ALA* 3.1 9.8 + - - +
97A VAL* 3.4 27.0 - - + +
98A THR* 2.9 29.5 + - - -
119A GLN* 3.4 8.6 - - - +
179A THR* 5.1 1.0 - - - +
182A LEU* 4.1 13.5 - - - +
225A ILE* 3.5 19.6 + - - +
226A ASN* 3.1 16.5 - - - +
227A PRO* 3.1 27.4 - - - +
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Residues in contact with ALA 95 (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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94A ASN* 1.3 74.0 + - - +
96A ALA* 1.3 56.2 + - - +
98A THR* 4.0 4.9 - - - -
99A PHE* 3.3 24.3 + - - +
112A PHE* 3.7 8.6 - - + -
116A VAL* 3.4 30.7 - - + -
119A GLN* 3.4 12.4 - - - +
226A ASN* 3.7 4.8 + - - +
227A PRO* 4.3 21.5 - - + -
228A SER* 5.0 4.7 - - - +
262A LEU* 4.5 6.4 - - + +
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Residues in contact with ALA 96 (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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94A ASN* 3.0 16.7 + - - +
95A ALA* 1.3 76.1 - - - +
97A VAL* 1.3 60.1 + - - +
98A THR 3.2 1.6 - - - -
99A PHE* 3.5 4.4 + - - +
100A ALA* 3.0 27.7 + - - +
179A THR* 4.5 1.6 - - + -
227A PRO* 4.1 7.3 - - + +
261A PRO* 3.5 34.5 - - + +
262A LEU* 3.8 11.6 - - - +
265A ALA* 3.5 12.9 - - + +
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Residues in contact with VAL 97 (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 ALA 5.2 0.2 - - - +
92A HIS* 3.4 39.7 + - + +
94A ASN* 3.3 28.6 + - + +
96A ALA* 1.3 76.3 - - + +
98A THR* 1.3 61.6 + - - +
100A ALA* 3.8 1.0 - - - +
101A ASN* 3.0 28.2 + - - +
179A THR* 6.1 0.2 - - + -
182A LEU* 4.2 17.0 - - + -
183A GLN* 3.4 29.6 + - + +
186A LEU* 4.4 19.1 - - + -
187A PHE* 5.7 0.3 - - - -
265A ALA* 5.1 1.6 - - + -
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Residues in contact with THR 98 (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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40A GLU* 4.9 0.2 + - - -
92A HIS* 2.9 42.1 + - + +
94A ASN 2.9 18.6 + - - -
95A ALA* 4.1 4.7 - - - -
97A VAL* 1.3 76.5 - - - +
99A PHE* 1.3 63.2 + - - +
100A ALA 3.2 0.2 - - - -
101A ASN* 3.3 2.1 + - - +
102A CYS* 2.8 36.6 + - - -
107A VAL* 5.0 1.1 - - + -
112A PHE* 3.5 30.1 - - + -
115A TYR* 4.4 14.0 - - + +
116A VAL* 6.5 0.4 - - - -
119A GLN* 4.1 5.5 + - - -
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Residues in contact with PHE 99 (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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95A ALA 3.3 13.6 + - - +
96A ALA 3.5 4.4 + - - +
98A THR* 1.3 77.9 - - - +
100A ALA* 1.3 60.0 + - - +
102A CYS* 3.8 7.0 + - + +
103A ALA* 3.5 25.7 + - + +
112A PHE* 3.5 39.6 - + + -
262A LEU* 4.0 40.2 - - + -
266A TYR* 5.4 11.7 - + + -
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Residues in contact with ALA 100 (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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96A ALA 3.0 17.4 + - - +
97A VAL 4.1 0.7 - - - +
98A THR 3.2 0.2 - - - -
99A PHE* 1.3 75.0 - - - +
101A ASN* 1.3 59.3 + - - +
102A CYS 3.3 1.8 - - - -
103A ALA* 3.9 4.7 - - - +
104A LEU* 3.0 33.0 + - + +
183A GLN* 3.5 23.6 - - + +
187A PHE* 4.6 6.0 - - + -
265A ALA 3.8 20.2 - - - +
266A TYR* 4.4 9.6 - - + +
269A GLY* 5.5 1.8 - - - -
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Residues in contact with ASN 101 (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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92A HIS* 3.6 23.6 + - + -
97A VAL 3.0 19.7 + - - +
98A THR* 3.3 7.4 + - - +
100A ALA* 1.3 75.8 - - - +
102A CYS* 1.3 59.2 + - - +
105A GLY* 2.8 51.8 + - - +
106A ARG 3.0 0.2 + - - -
107A VAL* 3.1 22.9 + - + +
187A PHE* 5.1 13.8 - - + -
401A GOL 4.3 4.2 + - - -
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Residues in contact with CYS 102 (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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98A THR* 2.8 30.9 + - - +
99A PHE* 4.0 10.3 - - + +
100A ALA 3.3 0.2 - - - -
101A ASN* 1.3 78.9 - - - +
103A ALA* 1.3 61.5 + - - +
104A LEU 3.6 0.2 + - - -
106A ARG* 3.9 11.6 + - - -
107A VAL* 3.0 33.0 - - + +
108A PRO 4.4 3.1 - - - -
109A TRP* 4.9 7.4 - - + -
112A PHE* 3.9 29.6 - - - -
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Residues in contact with ALA 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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99A PHE* 3.5 21.3 + - + +
100A ALA 3.7 1.8 + - - +
102A CYS* 1.3 78.5 - - + +
104A LEU* 1.3 60.7 + - - +
106A ARG 5.3 0.2 - - - -
266A TYR* 3.7 32.1 - - + -
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Residues in contact with LEU 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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100A ALA* 3.0 15.9 + - - +
101A ASN* 4.7 0.2 - - - -
103A ALA* 1.3 78.2 - - + +
105A GLY* 1.3 58.2 + - - +
106A ARG 3.8 0.9 - - - -
187A PHE* 3.7 19.7 - - + -
266A TYR* 5.9 4.3 - - + -
269A GLY* 3.6 25.6 - - - +
270A ILE* 4.7 8.5 - - + +
273A LEU* 3.7 38.9 - - + +
401A GOL 2.8 35.2 + - - +
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Residues in contact with GLY 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 ASN* 2.8 34.5 + - - +
104A LEU* 1.3 79.0 - - - +
106A ARG* 1.3 79.3 + - - +
107A VAL* 3.0 2.4 + - - -
187A PHE* 6.3 0.4 - - - -
401A GOL 3.5 21.1 + - - -
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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