Contacts of the strand formed by residues 117 - 124 (chain B) in PDB entry 4HXG
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU* 4.0 22.2 - - + +
111B TRP* 3.5 9.2 - - - -
112B ASN* 3.1 42.8 + - + +
114B ASP* 2.6 37.2 + - - +
116B ARG* 1.3 75.0 - - + +
118B LEU* 1.3 60.7 + - - +
156B VAL* 4.1 14.7 - - + +
157B ILE 3.0 8.1 - - - +
158B ASP* 4.7 0.4 - - - -
165B ILE* 3.8 31.0 - - + -
178B TRP* 4.3 13.8 - - + -
181B ASP* 3.0 39.8 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 5.8 0.7 - - + -
74B ALA* 4.3 14.8 - - + -
87B ILE* 4.2 23.8 - - + -
89B VAL* 5.0 0.7 - - + -
100B VAL* 5.8 0.4 - - + -
109B ILE* 4.9 12.8 - - + -
110B GLU 3.5 22.4 - - - +
111B TRP* 3.5 35.9 - - + +
117B ARG* 1.3 73.9 - - - +
119B LEU* 1.3 62.8 + - - +
120B ALA 3.9 0.4 - - - -
155B TRP 3.5 0.9 - - - +
156B VAL* 3.3 5.9 - - - +
157B ILE* 2.6 57.8 + - + +
159B THR* 3.8 24.5 - - + -
178B TRP* 4.1 4.3 - - - +
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Residues in contact with LEU 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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108B SER* 3.8 2.3 + - - +
109B ILE* 3.4 4.8 - - - -
110B GLU* 2.9 35.1 + - + +
118B LEU* 1.3 72.1 - - - +
120B ALA* 1.3 66.9 + - - +
121B VAL* 4.0 9.2 + - + -
154B PHE* 4.3 13.2 - - + -
155B TRP 3.3 16.8 - - - +
156B VAL* 4.8 1.8 - - + +
176B GLY* 4.0 8.5 - - - +
177B ILE* 4.0 37.5 - - - +
178B TRP* 3.2 27.3 - - + +
183B ILE* 3.9 31.2 - - + -
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Residues in contact with ALA 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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87B ILE* 5.0 0.2 - - + -
106B ILE* 3.7 22.9 - - + -
108B SER 3.3 8.5 - - - +
109B ILE* 4.3 7.6 - - + -
118B LEU 3.9 0.4 + - - -
119B LEU* 1.3 74.4 - - - +
121B VAL* 1.3 62.7 + - - +
154B PHE* 3.5 2.4 - - - -
155B TRP* 2.7 50.0 + - + +
157B ILE* 3.8 25.6 - - + -
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Residues in contact with VAL 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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106B ILE* 3.8 2.6 - - - -
107B ARG* 3.0 24.6 + - + -
108B SER* 3.2 33.1 + - - +
119B LEU* 4.4 9.0 - - + -
120B ALA* 1.3 76.4 - - - +
122B GLY* 1.3 62.6 + - - +
152B THR* 3.8 24.2 - - + -
153B THR 3.5 4.9 - - - +
154B PHE* 3.6 26.9 - - + -
155B TRP* 4.5 2.0 - - - -
174B SER 4.5 5.8 - - - +
175B SER* 4.9 3.6 - - - -
176B GLY 4.1 16.8 - - - +
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Residues in contact with GLY 122 (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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105B ASN 3.0 17.0 - - - -
107B ARG* 4.1 9.7 + - - -
121B VAL* 1.3 77.4 - - - +
123B PHE* 1.3 60.2 + - - +
152B THR* 3.4 11.6 - - - +
153B THR* 2.7 39.1 + - - +
155B TRP* 3.9 3.8 - - - -
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Residues in contact with PHE 123 (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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105B ASN* 3.0 73.7 + - + +
107B ARG* 3.1 43.7 - - + +
122B GLY* 1.3 75.9 - - - +
124B LYS* 1.3 64.1 + - - +
125B ARG* 3.6 46.0 - - + -
127B GLU* 5.3 1.8 - - - -
150B GLU* 3.5 22.7 - - + +
151B LYS 3.2 9.0 - - - +
152B THR* 4.9 0.4 - - - -
153B THR* 3.3 7.0 + - - -
155B TRP* 4.6 3.5 - - - -
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Residues in contact with LYS 124 (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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105B ASN* 4.9 2.9 - - - +
123B PHE* 1.3 76.1 - - - +
125B ARG* 1.3 68.9 + - - +
149B GLY 4.0 1.7 - - - +
150B GLU* 3.3 3.1 - - - -
151B LYS* 2.9 41.7 + - + +
153B THR* 4.0 18.1 - - + +
155B TRP* 6.1 0.4 - - + -
169B GLU* 4.6 12.8 - - - +
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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