Contacts of the strand formed by residues 120 - 130 (chain U) in PDB entry 1H2I
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 TYR 120 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26T PHE* 4.0 12.6 - + - -
84T TRP 4.9 0.4 + - - -
85T ALA* 2.9 45.9 - - + +
86T HIS* 3.1 30.7 + - - -
87T SER* 3.9 14.0 + - - -
112T ARG* 4.9 5.4 + - - -
114T GLN* 3.3 30.7 + - - +
112U ARG* 3.6 47.1 - - + +
113U VAL 3.3 15.3 - - - +
114U GLN* 4.2 1.6 - - - -
118U GLY 3.2 17.9 - - - -
119U SER* 1.3 76.3 - - - +
121U HIS* 1.3 68.4 + - - +
158U PHE* 4.7 3.3 - - - -
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Residues in contact with HIS 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T TYR 4.4 4.0 - - - -
84T TRP* 3.3 45.7 + + - -
86T HIS* 2.8 42.6 - + + -
112U ARG* 3.6 2.8 - - - -
113U VAL* 2.9 39.6 + - + +
120U TYR* 1.3 83.6 + - - +
122U GLU* 1.3 60.1 + - - +
154U ALA* 3.8 10.5 - - - +
157U SER* 3.3 36.5 - - - +
158U PHE* 3.6 34.2 - + - -
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Residues in contact with GLU 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T HIS* 2.9 29.7 + - - -
87T SER* 3.5 19.1 - - - -
88T ILE* 2.9 48.4 + - + +
147T VAL* 4.6 0.7 - - - +
89U THR* 2.6 40.2 + - - +
110U PHE* 3.8 5.6 - - - +
111U VAL 3.2 18.6 - - - +
112U ARG* 3.8 14.6 - - + +
121U HIS* 1.3 76.2 - - - +
123U ASP* 1.3 68.7 + - - +
154U ALA* 4.5 1.3 - - - -
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Residues in contact with ASP 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T HIS* 4.9 4.8 + - + +
88T ILE* 3.7 12.3 - - - -
147T VAL* 3.5 18.3 - - - +
148T THR* 5.2 2.3 + - - -
151T LEU* 6.2 0.2 - - - +
110U PHE* 3.4 3.5 - - - +
111U VAL* 3.0 32.2 + - - +
122U GLU* 1.3 77.6 - - - +
124U VAL* 1.3 70.6 + - - +
150U GLY* 4.5 2.0 - - - +
153U ARG* 2.4 55.0 + - + +
154U ALA* 3.8 22.6 - - + +
157U SER* 5.1 2.6 + - - -
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Residues in contact with VAL 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T ILE* 4.1 0.2 - - - +
91T GLN* 3.8 6.5 - - - +
143T ARG* 3.7 17.0 - - + +
144T LYS* 4.1 13.2 - - + -
147T VAL* 3.3 30.5 - - + -
108U CYS* 4.4 7.6 - - + -
109U ALA 3.2 8.7 - - - +
110U PHE* 3.1 38.6 - - + -
123U ASP* 1.3 86.5 + - - +
125U GLY* 1.3 65.7 + - - +
126U TYR* 6.4 0.2 - - + -
150U GLY* 4.0 2.9 - - - -
153U ARG* 2.9 29.3 + - - +
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Residues in contact with GLY 125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144T LYS* 4.4 1.1 - - - -
108U CYS* 3.3 7.6 - - - +
109U ALA 2.8 28.5 + - - +
124U VAL* 1.3 77.8 - - - +
126U TYR* 1.3 61.4 + - - +
146U ALA* 3.4 9.0 - - - -
149U ASP* 3.3 7.2 - - - -
150U GLY* 3.3 27.3 - - - -
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Residues in contact with TYR 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T ALA 3.6 15.3 - - - -
139T LEU* 3.4 19.0 - - + +
140T GLU* 3.5 47.0 - - + +
143T ARG* 3.8 12.8 - - + -
144T LYS* 4.0 4.3 - - + -
94U ASP* 2.6 33.4 + - - +
95U PHE* 4.0 0.9 - - - -
106U GLY* 3.3 30.9 - - - -
107U VAL 3.2 17.9 - - - -
108U CYS* 3.6 17.0 - - + -
125U GLY* 1.3 73.0 - - - -
127U GLY* 1.3 66.3 + - - +
128U VAL* 3.7 15.0 - - + +
145U GLU* 3.9 2.9 - - - +
146U ALA* 3.6 8.6 - - - +
149U ASP* 2.9 20.5 + - - +
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Residues in contact with GLY 127 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106U GLY* 3.6 1.4 - - - -
107U VAL 2.6 36.7 + - - -
126U TYR* 1.3 75.1 - - - +
128U VAL* 1.3 65.8 + - - +
142U ALA* 3.3 30.6 - - - +
145U GLU* 4.1 6.1 - - - -
146U ALA* 3.6 6.2 - - - +
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Residues in contact with VAL 128 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T ALA* 3.5 33.4 - - + -
137T LEU* 4.6 7.2 - - + -
140T GLU* 4.8 10.8 - - - +
105U VAL 3.4 3.4 - - - +
126U TYR* 3.7 20.6 - - + -
127U GLY* 1.3 79.9 - - - +
129U SER* 1.3 61.3 + - - +
130U GLU* 3.7 24.2 - - + +
141U LYS* 2.6 34.5 + - - +
142U ALA* 4.1 2.4 - - - +
145U GLU* 3.7 7.2 + - - +
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Residues in contact with SER 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U PHE 3.4 5.9 - - - +
105U VAL* 2.8 37.7 + - - +
128U VAL* 1.3 78.5 - - - +
130U GLU* 1.3 63.2 + - - +
132U LEU* 3.7 15.8 - - - +
138U SER* 3.4 47.5 + - - -
141U LYS* 3.9 14.2 - - - +
142U ALA 4.5 0.9 - - - -
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Residues in contact with GLU 130 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134T SER* 2.8 31.4 + - - -
135T LYS 4.9 0.3 + - - -
136T ALA* 3.9 8.0 + - + +
137T LEU* 3.8 11.4 - - - +
95U PHE* 5.7 0.2 - - - -
103U PHE 3.6 2.9 - - - -
104U TYR* 3.6 31.9 - - + +
105U VAL 4.9 0.2 - - - +
128U VAL* 3.7 20.3 - - + +
129U SER* 1.3 81.1 + - - +
131U GLY* 1.3 60.5 + - - +
132U LEU* 3.6 4.9 + - - +
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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