Contacts of the strand formed by residues 117 - 123 (chain A) in PDB entry 3HN3
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 THR 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.6 11.8 + - - +
111A TRP* 4.0 21.4 - - + -
114A ASP* 3.0 21.6 + - - +
115A LEU 4.1 2.8 - - - +
116A ARG* 1.3 77.8 - - - +
118A ARG* 1.3 63.7 + - - +
119A VAL* 4.0 10.0 + - + -
154A SER* 3.8 5.0 + - - -
158A GLN* 2.9 22.3 + - - +
222A THR* 3.8 32.5 - - + -
223A THR 4.1 2.9 - - - +
225A THR* 4.3 3.5 - - - +
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Residues in contact with ARG 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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116A ARG 3.7 1.0 + - - -
117A THR* 1.3 71.6 - - - +
119A VAL* 1.3 61.8 + - - +
120A VAL* 3.6 25.6 + - + +
150A GLU* 4.2 14.3 + - - -
152A ASP* 3.1 35.7 + - - +
154A SER* 3.3 4.0 - - - +
221A TYR* 3.8 3.7 + - - +
222A THR* 3.1 9.4 - - - -
223A THR* 2.8 65.2 + - - +
224A PRO 3.6 7.6 - - - +
225A THR* 4.3 9.6 - - + +
227A TYR* 3.3 56.7 + - - -
229A ASP* 5.0 1.4 + - - -
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Residues in contact with VAL 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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107A LEU* 4.8 1.6 - - + -
111A TRP* 4.1 41.7 - - + +
117A THR* 4.1 11.4 - - + +
118A ARG* 1.3 75.0 - - - +
120A VAL* 1.3 58.5 + - - +
152A ASP* 3.4 5.2 - - - +
153A ILE* 2.8 57.3 + - + -
154A SER* 2.8 16.5 + - - +
157A VAL* 3.9 25.8 - - + -
220A LEU* 4.2 12.1 - - + -
221A TYR 3.7 3.6 - - - +
222A THR* 4.5 0.4 - - + -
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Residues in contact with VAL 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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118A ARG* 3.6 42.4 - - + +
119A VAL* 1.3 79.0 - - - +
121A LEU* 1.3 63.3 + - - +
122A ARG 3.9 0.3 + - - -
150A GLU* 3.4 27.1 - - + +
151A ALA 3.5 12.6 - - - +
152A ASP* 4.7 1.6 - - - -
219A LEU 3.9 0.3 - - - +
220A LEU* 3.2 10.3 - - - +
221A TYR* 2.8 75.0 + - + +
223A THR* 5.3 0.7 - - + -
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Residues in contact with LEU 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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41A LEU* 4.4 0.9 - - + -
119A VAL 4.3 0.2 + - - -
120A VAL* 1.3 72.3 - - - +
122A ARG* 1.3 59.6 + - - +
123A ILE* 4.2 10.0 + - + -
132A VAL* 3.7 29.6 - - + -
134A VAL* 4.3 15.0 - - + -
139A THR* 6.2 0.9 - - + -
140A LEU* 4.3 7.6 - - + +
149A PHE 4.1 0.5 - - - +
150A GLU* 3.1 4.5 - - - -
151A ALA* 3.0 35.4 + - + +
153A ILE* 4.1 12.7 - - + +
168A ILE* 3.8 35.4 - - + -
218A VAL* 4.3 17.7 - - + -
219A LEU 3.7 11.7 - - - +
220A LEU* 3.9 15.0 - - + +
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Residues in contact with ARG 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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27A MET* 3.5 27.2 + - - +
28A LEU 2.9 26.1 + - - +
29A TYR* 4.5 3.0 - - - +
30A PRO* 3.4 25.7 - - + +
120A VAL 3.9 0.4 + - - -
121A LEU* 1.3 73.1 - - - +
123A ILE* 1.3 71.5 + - - +
124A GLY* 4.6 2.5 - - - +
148A PRO* 4.1 11.5 - - - +
149A PHE 3.7 14.1 - - - -
150A GLU* 3.0 29.2 + - + +
218A VAL* 3.4 6.4 - - - +
219A LEU* 2.9 58.8 + - + +
221A TYR* 4.0 21.3 + - + -
390A GLU* 4.1 17.4 + - - -
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Residues in contact with ILE 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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121A LEU* 4.3 15.3 - - + -
122A ARG* 1.3 76.4 - - - +
124A GLY* 1.3 64.9 + - - +
125A SER 3.4 20.4 + - - +
132A VAL* 4.4 8.5 - - + -
140A LEU* 4.4 4.9 - - + -
148A PRO* 3.3 2.4 - - - +
149A PHE* 2.9 72.3 + - + +
170A ILE* 3.7 21.3 - - + -
214A LEU* 4.1 16.2 - - + -
217A SER 4.5 0.7 - - - -
218A VAL* 3.6 27.6 - - + -
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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