Contacts of the strand formed by residues 145 - 152 (chain H) in PDB entry 1XFB
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 PHE 145 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ILE* 3.6 31.6 - - + -
30H ILE* 4.4 7.4 - - + -
76H GLY* 4.3 6.1 - - - -
77H VAL 3.7 22.0 - - - -
78H ILE* 3.6 20.0 - - + -
104H VAL* 3.6 20.9 - - + -
105H VAL 3.2 19.7 - - - -
106H GLY* 2.9 42.0 - - - -
107H ILE* 3.2 8.5 + - - +
143H ALA 3.7 0.4 - - - -
144H ASP* 1.3 81.7 - - - +
146H ALA* 1.3 62.0 + - - +
183H ILE* 3.7 5.6 - - - +
184H VAL* 2.9 21.3 - - + +
186H ILE* 3.6 34.3 - - + -
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Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ILE* 3.2 17.7 - - + +
109H VAL* 3.9 17.3 - - + -
135H CYS* 5.7 0.4 - - - -
145H PHE* 1.3 78.9 - - - +
147H LYS* 1.3 61.7 + - - +
174H TYR* 3.2 10.1 - - + +
178H CYS* 4.1 11.4 - - - -
183H ILE* 3.9 14.1 - - + -
184H VAL 2.8 7.7 + - - +
186H ILE* 2.8 31.9 + - - +
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Residues in contact with LYS 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ALA* 5.1 0.6 - - - +
34H ASP* 3.2 32.9 + - - +
78H ILE* 4.0 28.3 - - + -
107H ILE 3.0 5.3 + - - -
108H LYS* 3.4 11.9 - - - +
109H VAL* 3.0 27.5 + - - +
110H ASP* 3.9 2.0 + - - +
146H ALA* 1.3 77.8 - - - +
148H TRP* 1.3 63.2 + - - +
149H ARG* 4.2 15.4 - - - +
174H TYR* 3.3 4.5 - - - -
186H ILE* 4.0 8.7 - - + +
188H GLU* 2.8 30.1 + - - +
230H LYS* 3.0 32.1 - - + +
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Residues in contact with TRP 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H VAL* 4.0 2.9 - - + -
110H ASP* 3.6 23.6 - - + -
125H THR* 3.3 36.5 - - + -
126H GLN 3.5 0.4 - - - -
127H GLY* 3.4 27.6 - - - -
128H LEU* 3.4 39.7 - - + -
131H LEU* 4.4 4.7 - - + -
147H LYS* 1.3 76.3 - - - +
149H ARG* 1.3 63.2 + - - +
150H CYS* 3.6 13.3 - - - -
170H VAL* 3.3 25.3 - - + +
171H LEU* 3.6 18.0 - - + +
174H TYR* 3.3 50.1 + + + -
186H ILE 3.7 1.6 + - - -
188H GLU* 3.3 25.5 + - - +
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Residues in contact with ARG 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H LYS* 5.7 2.9 - - - +
110H ASP* 3.2 18.4 + - - +
113H VAL* 5.6 1.9 + - - +
125H THR* 2.8 21.2 + - - +
147H LYS* 4.2 11.2 - - - +
148H TRP* 1.3 76.4 - - - +
150H CYS* 1.3 69.7 + - - +
151H VAL* 3.4 31.4 - - + +
188H GLU* 3.3 32.5 - - + +
190H GLU* 2.4 44.5 + - - +
192H LEU* 4.3 7.3 - - - +
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Residues in contact with CYS 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H THR* 3.3 10.5 - - - -
148H TRP* 3.6 23.7 + - - -
149H ARG* 1.3 77.6 - - - +
151H VAL* 1.3 66.6 + - - +
152H LEU* 5.6 1.8 - - + -
167H ASN* 3.3 35.9 - - + +
170H VAL* 4.6 3.1 - - - -
171H LEU* 3.6 26.5 - - + -
188H GLU 3.0 13.2 + - - +
189H PRO* 4.5 7.0 - - + -
190H GLU* 3.2 21.9 + - - +
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Residues in contact with VAL 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H VAL* 4.7 12.9 - - + +
123H THR* 3.5 30.4 + - - +
124H THR 5.9 0.2 - - - -
125H THR* 4.5 1.4 + - - -
149H ARG* 3.4 40.2 - - + +
150H CYS* 1.3 82.2 - - - +
152H LEU* 1.3 72.7 + - - +
153H LYS* 5.9 0.2 - - + -
167H ASN* 4.2 3.5 + - - +
190H GLU 3.4 4.0 - - - +
192H LEU* 3.5 39.9 - - + -
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Residues in contact with LEU 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H GLU* 5.5 1.3 - - - +
123H THR 5.2 0.2 - - - +
150H CYS* 5.6 1.6 - - + -
151H VAL* 1.3 79.1 - - - +
153H LYS* 1.3 59.2 + - - +
159H PRO* 5.0 8.5 - - + -
163H ALA* 3.8 19.1 - - + +
164H ILE* 4.6 13.2 - - + -
167H ASN* 3.5 34.1 - - + +
189H PRO* 5.6 5.4 - - + -
190H GLU 2.8 12.7 + - - +
191H ILE* 4.2 13.0 - - + -
192H LEU* 2.9 31.5 + - - +
209H VAL* 3.3 46.7 - - + -
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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