Contacts of the helix formed by residues 112 - 129 (chain A) in PDB entry 1N1F
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 ARG 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.5 27.1 - - - +
54A LEU* 3.3 42.3 - - + +
55A ASP* 2.9 36.8 + - - +
110A HIS* 3.6 12.6 + - + -
111A CYS* 1.3 74.1 - - - +
113A GLN* 1.3 67.5 + - - +
114A GLU* 3.2 9.1 - - + +
115A ALA* 3.0 8.0 + - - +
116A THR* 3.0 18.5 + - - -
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Residues in contact with GLN 113 (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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111A CYS 3.8 1.2 + - - -
112A ARG* 1.3 73.4 - - - +
114A GLU* 1.3 56.6 + - - +
116A THR* 3.7 15.5 + - - +
117A ASN* 2.8 69.9 + - - +
120A ARG* 3.7 18.1 + - - +
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Residues in contact with GLU 114 (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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49A GLN* 4.0 37.8 - - - +
50A ILE* 4.7 4.0 - - + -
55A ASP* 5.1 9.0 - - - +
112A ARG* 3.1 8.0 + - + +
113A GLN* 1.3 74.8 - - - +
115A ALA* 1.3 62.6 + - - +
117A ASN* 3.8 7.9 - - - +
118A ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 115 (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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50A ILE* 4.0 13.2 - - - -
55A ASP* 4.0 21.9 + - + +
58A CYS* 3.5 29.4 - - + -
59A VAL* 4.0 10.2 - - + +
112A ARG* 3.0 12.5 + - - +
114A GLU* 1.3 75.9 - - - +
116A THR* 1.3 66.2 + - - +
118A ALA* 3.2 3.1 + - - +
119A THR* 3.0 27.3 + - - -
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Residues in contact with THR 116 (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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62A ASN* 4.8 5.1 + - - +
111A CYS* 3.4 22.2 + - - +
112A ARG 3.0 12.6 + - - -
113A GLN* 3.6 19.4 + - - +
115A ALA* 1.3 78.9 - - - +
117A ASN* 1.3 62.5 + - - +
119A THR* 3.3 8.4 + - - -
120A ARG* 2.9 59.2 + - + +
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Residues in contact with ASN 117 (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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113A GLN* 2.8 53.4 + - - +
114A GLU* 3.8 8.2 - - - +
115A ALA 3.2 0.2 - - - -
116A THR* 1.3 76.9 - - - +
118A ALA* 1.3 64.2 + - - +
120A ARG* 3.0 21.6 + - - +
121A VAL* 2.9 30.2 + - + +
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Residues in contact with ALA 118 (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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44A THR* 2.6 47.2 + - + -
49A GLN* 4.1 10.3 - - + +
50A ILE* 3.6 17.3 - - + -
59A VAL* 4.8 2.2 - - + -
114A GLU* 3.0 20.4 + - - +
115A ALA 3.5 5.6 - - - +
117A ASN* 1.3 77.5 - - - +
119A THR* 1.3 60.7 + - - +
121A VAL* 3.5 12.7 - - - +
122A ILE* 3.7 3.7 + - - +
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Residues in contact with THR 119 (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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59A VAL* 4.0 12.5 - - - +
62A ASN* 2.9 48.5 + - + +
63A LEU* 5.9 2.8 - - + +
115A ALA 3.0 10.7 + - - -
116A THR* 3.3 9.2 - - - +
118A ALA* 1.3 76.9 - - - +
120A ARG* 1.3 67.9 + - + +
122A ILE* 3.1 22.4 + - + +
123A HIS* 3.3 29.2 + - + +
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Residues in contact with ARG 120 (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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113A GLN* 3.7 10.3 + - - +
116A THR* 2.9 42.7 + - + +
117A ASN* 3.0 26.8 + - - +
119A THR* 1.3 75.9 - - + +
121A VAL* 1.3 56.2 + - - +
123A HIS* 3.1 9.3 + - + +
124A ASP* 2.7 49.9 + - - +
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Residues in contact with VAL 121 (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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43A SER* 3.4 25.1 - - - +
44A THR* 4.1 6.1 - - - +
49A GLN* 5.9 1.6 - - - +
117A ASN* 2.9 21.2 + - + +
118A ALA* 3.5 12.8 - - - +
120A ARG* 1.3 75.7 - - - +
122A ILE* 1.3 52.6 + - - +
124A ASP* 3.2 9.7 + - - +
125A ASN* 2.7 46.2 + - - +
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Residues in contact with ILE 122 (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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41A ILE* 3.6 23.3 - - + +
42A LEU* 3.9 30.3 - - + -
44A THR* 3.7 31.9 - - + +
45A LEU* 4.5 4.0 - - + -
59A VAL* 5.8 1.3 - - + -
63A LEU* 3.6 28.0 - - + -
66A PHE* 4.0 28.0 - - + -
118A ALA 4.0 4.7 - - - +
119A THR* 3.1 13.1 + - + +
121A VAL* 1.3 74.9 - - - +
123A HIS* 1.3 67.4 + - + +
125A ASN* 3.0 3.1 + - - +
126A TYR* 2.9 22.0 + - - +
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Residues in contact with HIS 123 (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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62A ASN* 5.0 2.6 + - - +
66A PHE* 3.6 29.4 - + + +
70A ARG* 3.1 47.0 + - + +
119A THR* 3.3 35.1 + - + +
120A ARG* 3.1 11.7 + - + +
122A ILE* 1.3 80.7 - - + +
124A ASP* 1.3 60.5 + - - +
126A TYR* 3.2 6.2 + - - +
127A ASP* 2.8 38.8 + - - +
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Residues in contact with ASP 124 (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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120A ARG* 2.7 32.5 + - - +
121A VAL* 3.3 9.6 - - - +
123A HIS* 1.3 79.8 - - - +
125A ASN* 1.3 68.5 + - - +
127A ASP* 3.3 14.9 + - - +
128A GLN* 3.4 22.9 + - - +
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Residues in contact with ASN 125 (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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39A VAL* 6.3 2.5 - - + -
40A THR 3.7 7.0 + - - +
41A ILE* 3.0 31.3 + - + +
43A SER* 2.9 27.9 + - - -
121A VAL* 2.7 29.7 + - - +
122A ILE 3.0 5.1 + - - +
124A ASP* 1.3 74.2 - - - +
126A TYR* 1.3 64.0 + - - +
128A GLN* 3.1 30.4 + - - +
129A LEU* 3.8 8.8 - - - +
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Residues in contact with TYR 126 (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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41A ILE* 4.2 10.9 - - + +
66A PHE* 3.5 22.9 - + + -
70A ARG* 3.5 33.9 - - + -
71A VAL* 3.7 14.3 - - + -
74A ASP* 2.6 40.9 + - - +
122A ILE 2.9 12.0 + - - +
123A HIS* 3.4 10.1 - - - +
125A ASN* 1.3 78.4 - - - +
127A ASP* 1.3 59.4 + - - +
128A GLN 3.1 4.7 + - - -
129A LEU* 3.2 12.6 + - - +
131A VAL* 4.1 6.9 + - + -
134A ALA* 3.4 40.0 - - + +
135A ALA* 3.5 11.8 - - - +
138A SER* 3.2 27.6 - - - -
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Residues in contact with ASP 127 (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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70A ARG* 2.5 39.6 + - - -
123A HIS* 2.8 25.4 + - - +
124A ASP* 3.3 9.4 + - - +
125A ASN 3.3 0.2 - - - -
126A TYR* 1.3 74.1 - - - +
128A GLN* 1.3 65.3 + - - +
129A LEU 3.2 6.1 + - - +
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Residues in contact with GLN 128 (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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124A ASP* 3.4 23.0 + - - +
125A ASN* 3.1 22.8 + - - +
126A TYR 3.0 0.4 - - - -
127A ASP* 1.3 81.8 - - - +
129A LEU* 1.3 69.9 + - + +
130A GLU 4.3 0.2 + - - -
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Residues in contact with LEU 129 (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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36A PHE* 3.7 41.5 - - + -
39A VAL* 5.6 5.6 - - + -
41A ILE* 3.9 28.0 - - + -
125A ASN 3.8 15.0 - - - +
126A TYR 3.2 13.4 + - - +
127A ASP* 4.0 5.9 - - - +
128A GLN* 1.3 94.1 - - + +
130A GLU* 1.3 75.2 + - - +
131A VAL* 3.3 3.3 + - - -
133A ALA* 4.6 5.4 - - + -
134A ALA* 4.0 12.1 - - + +
137A LYS* 4.4 10.3 - - + -
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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