Contacts of the helix formed by residues 111 - 121 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B VAL 3.6 6.7 + - - +
107B VAL* 3.1 14.4 + - - +
110B ASN* 1.3 79.4 - - - +
112B LEU* 1.3 65.9 + - - +
114B SER* 3.5 7.2 + - - -
115B LEU* 3.7 13.7 - - - +
131B ARG* 4.8 1.9 + - - +
134B ALA* 3.7 34.5 - - + +
135B ILE* 4.1 15.3 - - + +
138B ALA* 4.8 1.6 - - + -
171B LEU* 4.1 14.0 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.8 11.7 - - + -
107B VAL 2.9 11.9 + - - +
108B PHE* 3.5 27.4 - - + +
111B ALA* 1.3 76.7 - - - +
113B ARG* 1.3 68.7 + - - +
115B LEU* 3.2 3.8 + - - +
116B ALA* 2.8 34.3 + - + +
167B SER* 3.7 27.8 - - - +
170B SER* 3.6 28.9 - - - -
171B LEU* 3.9 16.8 - - + -
174B PHE* 4.7 3.5 - - + -
208B PHE* 4.1 22.9 - - + -
301B GSH 5.9 1.6 - - - -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 6.4 2.5 - - - -
110A ASN* 5.0 15.2 + - - +
108B PHE* 2.8 51.7 + - + +
109B ALA* 4.2 9.2 - - - +
112B LEU* 1.3 79.3 - - - +
114B SER* 1.3 57.8 + - - +
116B ALA* 4.0 2.9 - - - +
117B LYS* 2.8 52.8 + - + +
301B GSH 3.7 37.5 + - - -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 5.6 4.3 - - - -
109B ALA 3.7 9.7 + - - -
110B ASN* 2.9 26.0 + - - -
111B ALA 3.5 5.9 + - - -
113B ARG* 1.3 80.4 - - - +
115B LEU* 1.3 66.5 + - - -
117B LYS* 3.5 7.2 + - - +
118B MET* 3.3 24.1 + - - +
131B ARG* 3.3 24.9 + - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA 3.7 13.2 - - - +
112B LEU 3.2 2.5 + - - +
114B SER* 1.3 79.4 + - - +
116B ALA* 1.3 65.6 + - - +
118B MET* 3.2 5.7 + - - +
119B ILE* 3.0 33.3 + - + +
127B VAL* 3.7 37.2 - - + -
131B ARG* 4.0 21.3 - - + +
132B ILE* 4.2 14.6 - - + -
135B ILE* 3.8 17.9 - - + -
174B PHE* 3.5 41.1 - - + -
217B PHE* 4.6 2.9 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 2.8 23.7 + - + +
113B ARG* 4.0 3.8 - - - +
115B LEU* 1.3 77.0 - - - +
117B LYS* 1.3 57.2 + - - +
119B ILE* 4.7 0.7 - - - -
120B LEU* 2.7 58.0 + - + +
121B PHE* 5.0 2.9 - - + -
174B PHE* 4.1 9.1 - - + -
208B PHE* 4.2 18.6 - - + -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU* 6.2 2.0 - - - +
137A GLU* 5.0 11.7 + - - -
113B ARG* 2.8 40.5 + - + +
114B SER* 3.7 7.0 - - - +
116B ALA* 1.3 75.4 - - - +
118B MET* 1.3 59.0 + - + +
121B PHE* 3.0 32.5 + - + +
122B LEU* 2.9 54.9 + - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER 3.3 9.6 + - - +
115B LEU* 3.2 10.0 + - - +
117B LYS* 1.3 78.9 - - + +
119B ILE* 1.3 64.3 + - + +
122B LEU* 3.5 15.9 + - + -
123B GLY 3.2 9.9 + - - -
124B LYS* 2.9 45.5 + - + +
126B GLU 4.0 8.1 - - - +
127B VAL* 3.7 24.5 - - + -
128B PRO* 3.9 17.3 - - + -
131B ARG* 4.0 28.3 - - - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.0 29.2 + - + +
116B ALA* 4.0 2.2 - - - +
118B MET* 1.3 76.5 - - - +
120B LEU* 1.3 74.3 + - + +
121B PHE 3.5 0.2 - - - -
123B GLY* 4.0 12.0 + - - -
124B LYS 3.7 18.9 + - - +
127B VAL* 3.7 25.8 - - + -
174B PHE* 4.4 3.8 - - + -
212B VAL* 4.6 9.2 - - + +
215B LYS* 3.3 47.4 - - + +
217B PHE* 3.6 28.7 - - + -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B MET* 5.0 11.0 - - + +
116B ALA* 2.7 36.0 + - + +
119B ILE* 1.3 80.7 - - + +
121B PHE* 1.3 75.5 + - + +
123B GLY* 4.9 0.7 - - - -
208B PHE* 4.2 13.5 - - + -
211B ALA* 3.5 42.4 - - + +
212B VAL* 3.9 25.4 - - + +
215B LYS* 4.1 22.6 + - + +
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 5.6 14.4 - - + -
37B MET* 3.5 33.7 - - + -
116B ALA* 4.8 2.9 - - + -
117B LYS* 3.0 36.0 + - + +
120B LEU* 1.3 93.1 - - + +
122B LEU* 1.3 72.5 + - + +
123B GLY 3.4 2.2 - - - -
301B GSH 5.7 10.1 - - - -
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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