Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 4HI7
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 ALA 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A VAL 3.6 6.9 + - - +
107A VAL* 3.0 14.9 + - - +
110A ASN* 1.3 79.0 - - - +
112A LEU* 1.3 64.6 + - - +
114A SER* 3.4 7.3 + - - -
115A LEU* 3.8 12.3 - - - +
131A ARG* 4.8 2.2 + - - +
134A ALA* 3.6 34.8 - - + +
135A ILE* 4.1 16.3 - - + +
138A ALA* 4.9 1.1 - - + -
171A LEU* 3.9 14.6 - - + +
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Residues in contact with LEU 112 (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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13A PRO* 3.9 15.5 - - + -
107A VAL 2.9 11.5 + - - +
108A PHE* 3.2 28.7 + - + +
111A ALA* 1.3 76.2 - - - +
113A ARG* 1.3 65.8 + - - +
114A SER 3.2 2.0 - - - -
115A LEU* 3.2 4.4 + - - +
116A ALA* 2.9 32.7 + - + +
167A SER* 3.4 43.5 - - - +
170A SER* 3.6 17.3 - - - -
171A LEU* 3.8 18.6 - - + +
174A PHE* 4.8 1.9 - - + -
208A PHE* 4.2 19.3 - - + -
301A GSH 5.9 0.9 - - - -
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Residues in contact with ARG 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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53A HIS* 6.1 0.8 - - - -
54A THR* 4.7 3.2 - - - +
108A PHE* 2.8 50.9 + - + +
109A ALA* 4.4 6.5 - - - +
112A LEU* 1.3 79.0 - - - +
114A SER* 1.3 56.6 + - - +
116A ALA* 4.1 2.9 - - - +
117A LYS* 2.8 59.0 + - + +
301A GSH 2.8 66.9 + - - -
106B VAL* 6.3 3.8 - - - -
141B PHE* 6.1 3.0 - - - -
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Residues in contact with SER 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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109A ALA 3.8 10.5 + - - -
110A ASN 2.8 28.1 + - - -
111A ALA 3.4 8.0 + - - -
113A ARG* 1.3 81.0 - - - +
115A LEU* 1.3 66.3 + - - -
117A LYS* 4.0 3.4 - - - +
118A MET* 3.3 25.9 + - - +
131A ARG* 3.3 22.4 + - - -
110B ASN* 5.6 4.7 - - - -
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Residues in contact with LEU 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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111A ALA 3.8 13.0 - - - +
112A LEU 3.2 2.6 + - - +
114A SER* 1.3 78.6 + - - +
116A ALA* 1.3 66.4 + - - +
118A MET* 3.2 11.1 + - + +
119A ILE* 3.1 31.9 + - + +
127A VAL* 3.5 40.8 - - + -
131A ARG* 4.1 17.7 - - + +
132A ILE* 4.5 8.3 - - + -
135A ILE* 3.9 19.3 - - + -
174A PHE* 3.5 44.2 - - + -
217A PHE* 5.5 1.1 - - + -
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Residues in contact with ALA 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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112A LEU* 2.9 22.6 + - + +
113A ARG* 4.1 3.1 - - - +
115A LEU* 1.3 75.5 - - - +
117A LYS* 1.3 60.1 + - - +
119A ILE* 4.7 0.4 - - - -
120A LEU* 2.8 46.2 + - + +
121A PHE* 3.9 4.4 - - + -
174A PHE* 4.3 8.7 - - + -
208A PHE* 3.9 32.3 - - + -
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Residues in contact with LYS 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 ARG* 2.8 47.8 + - + +
114A SER* 4.0 3.8 - - - +
116A ALA* 1.3 75.6 - - - +
118A MET* 1.3 62.2 + - - +
121A PHE* 3.0 29.0 + - + +
122A LEU* 3.0 50.4 + - + +
137B GLU* 4.7 17.4 + - - -
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Residues in contact with MET 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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114A SER 3.3 17.1 + - - +
115A LEU* 3.2 11.3 + - + +
117A LYS* 1.3 80.6 - - - +
119A ILE* 1.3 57.8 + - - +
122A LEU* 3.5 13.3 + - + +
123A GLY 3.3 10.2 + - - -
124A LYS* 3.1 45.6 + - + +
126A GLU 3.6 24.0 - - - +
127A VAL* 3.7 27.1 - - + -
128A PRO* 4.0 7.4 - - + -
131A ARG* 4.1 22.9 - - - -
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Residues in contact with ILE 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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115A LEU* 3.1 25.9 + - + +
116A ALA* 4.2 2.2 - - - +
118A MET* 1.3 80.0 - - + +
120A LEU* 1.3 73.4 - - + +
121A PHE 3.6 0.2 - - - -
123A GLY* 4.3 8.3 + - - -
124A LYS 3.7 21.3 - - - +
127A VAL* 3.6 28.3 - - + -
174A PHE* 4.3 11.7 - - + -
212A VAL* 4.7 7.9 - - + +
215A LYS* 3.4 49.7 - - + +
217A PHE* 3.9 17.5 - - + -
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Residues in contact with LEU 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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37A MET* 4.1 26.1 - - + +
116A ALA* 2.8 33.8 + - + +
119A ILE* 1.3 88.5 - - + +
121A PHE* 1.3 73.5 + - + +
123A GLY 5.0 0.4 - - - -
208A PHE* 4.3 17.0 - - + -
211A ALA* 3.5 45.1 - - + +
212A VAL* 3.9 15.7 - - + +
215A LYS* 4.1 22.4 + - + +
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Residues in contact with PHE 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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36A LEU* 4.1 38.6 - - + -
37A MET* 3.6 37.0 - - + -
41A GLN* 5.9 1.3 - - - -
116A ALA* 3.9 5.4 - - + -
117A LYS* 3.0 37.1 + - + +
120A LEU* 1.3 92.2 - - + +
122A LEU* 1.3 68.8 + - + +
123A GLY 3.5 1.6 - - - -
301A GSH 6.0 2.7 - - - -
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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