Contacts of the strand formed by residues 120 - 132 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26S PHE* 4.0 12.8 - + - -
84S TRP 4.9 0.4 + - - -
85S ALA* 2.7 52.5 - - + +
86S HIS 3.5 27.4 - - - -
87S SER* 3.9 13.9 + - - -
112S ARG* 4.9 6.4 + - - -
114S GLN* 3.3 30.4 + - - +
112T ARG* 3.5 46.7 - - + +
113T VAL 3.2 14.8 - - - +
114T GLN* 4.2 1.1 - - - -
118T GLY 3.2 17.5 - - - +
119T SER* 1.3 75.6 - - - +
121T HIS* 1.3 71.5 + - - +
158T PHE* 4.8 3.1 - - - -
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Residues in contact with HIS 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S TYR 4.4 4.3 - - - -
84S TRP* 3.3 46.8 + + - -
86S HIS* 2.8 41.5 - + + -
112T ARG* 3.6 1.7 - - - -
113T VAL* 2.9 38.5 + - + +
120T TYR* 1.3 83.7 + - - +
122T GLU* 1.3 62.0 + - - +
154T ALA* 3.7 11.2 - - - +
157T SER* 3.4 33.5 - - - -
158T PHE* 3.5 35.6 - + - -
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Residues in contact with GLU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S HIS* 3.0 39.2 + - - +
87S SER* 3.4 12.3 - - - -
88S ILE* 2.8 49.0 + - + +
147S VAL* 4.6 0.5 - - - +
89T THR* 2.6 38.7 + - - +
110T PHE* 3.8 5.6 - - - +
111T VAL 3.2 17.7 - - - +
112T ARG* 3.9 13.5 - - + +
121T HIS* 1.3 77.3 - - - +
123T ASP* 1.3 67.1 + - - +
154T ALA* 4.5 0.4 - - - -
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Residues in contact with ASP 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S HIS* 5.1 4.4 + - + +
88S ILE* 3.8 11.7 - - - -
147S VAL* 3.3 21.0 - - - +
148S THR* 5.1 2.3 + - - -
110T PHE* 3.5 2.9 - - - +
111T VAL* 3.0 32.8 + - - +
122T GLU* 1.3 76.6 - - - +
124T VAL* 1.3 72.8 + - - +
150T GLY 4.4 1.4 - - - +
153T ARG* 2.6 52.6 + - + +
154T ALA* 3.8 23.5 - - + +
157T SER* 5.2 2.4 + - - -
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Residues in contact with VAL 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE* 4.1 0.2 - - - +
91S GLN* 3.9 6.5 - - - +
143S ARG* 3.9 20.2 - - + +
144S LYS* 4.3 4.6 - - + -
147S VAL* 3.2 30.7 - - + -
108T CYS* 4.5 7.0 - - + -
109T ALA 3.2 8.7 - - - +
110T PHE* 3.1 38.8 - - + -
123T ASP* 1.3 80.2 + - - +
125T GLY* 1.3 64.1 + - - +
126T TYR* 6.2 0.4 - - + -
150T GLY* 4.0 2.2 - - - -
153T ARG* 2.8 34.9 + - - +
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Residues in contact with GLY 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144S LYS* 4.6 1.6 - - - -
108T CYS* 3.2 7.6 - - - +
109T ALA 2.8 29.9 + - - -
124T VAL* 1.3 78.1 - - - +
126T TYR* 1.3 61.2 + - - +
146T ALA 3.4 8.1 - - - -
149T ASP* 3.4 6.3 - - - -
150T GLY* 3.3 27.5 - - - -
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Residues in contact with TYR 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S ALA* 3.8 13.7 - - - -
139S LEU* 3.4 18.7 - - + +
140S GLU* 3.8 43.6 - - + +
143S ARG* 3.8 14.1 - - + -
144S LYS* 4.1 4.9 - - + +
94T ASP* 2.6 36.1 + - - +
95T PHE* 4.0 2.3 - - - -
106T GLY* 3.4 28.9 - - - -
107T VAL 3.3 15.5 - - - -
108T CYS* 3.6 17.7 - - + -
124T VAL* 6.2 0.4 - - + -
125T GLY* 1.3 73.4 - - - -
127T GLY* 1.3 68.7 + - - +
128T VAL* 3.7 16.4 + - + +
145T GLU* 3.9 3.1 - - - +
146T ALA* 3.6 5.0 - - - -
149T ASP* 2.8 25.7 + - - +
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Residues in contact with GLY 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T GLY* 3.6 1.2 - - - -
107T VAL 2.6 38.0 + - - +
126T TYR* 1.3 74.4 - - - +
128T VAL* 1.3 66.0 + - - +
142T ALA* 3.2 29.8 - - - +
145T GLU* 4.1 6.5 - - - -
146T ALA* 3.5 6.1 - - - +
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Residues in contact with VAL 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S ALA* 3.7 33.0 - - + +
137S LEU* 5.0 6.5 - - + -
140S GLU* 5.0 9.4 - - - +
105T VAL 3.4 4.0 - - - +
126T TYR* 3.7 19.5 - - + +
127T GLY* 1.3 79.9 - - - +
129T SER* 1.3 61.6 + - - +
130T GLU* 3.8 24.9 - - + +
141T LYS* 2.6 34.7 + - - +
142T ALA* 4.0 3.7 - - - +
145T GLU* 3.8 6.7 + - - +
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Residues in contact with SER 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103T PHE 3.3 6.0 - - - +
105T VAL* 2.8 35.9 + - - +
128T VAL* 1.3 78.8 - - - +
130T GLU* 1.3 61.6 + - - +
132T LEU* 3.7 15.4 - - - +
138T SER* 3.4 46.5 + - - -
141T LYS* 3.8 15.5 - - - +
142T ALA* 4.3 1.1 - - - +
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Residues in contact with GLU 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134S SER* 2.9 29.1 + - - -
135S LYS 4.9 0.9 + - - -
136S ALA* 3.8 9.7 + - + +
137S LEU* 4.0 8.7 - - - +
95T PHE* 5.8 0.2 - - - -
103T PHE 3.5 2.7 - - - -
104T TYR* 3.6 31.4 - - + +
105T VAL 4.9 0.4 - - - +
128T VAL* 3.8 23.0 - - + +
129T SER* 1.3 78.5 + - - +
131T GLY* 1.3 60.1 + - - +
132T LEU* 3.6 5.4 + - - +
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Residues in contact with GLY 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T LYS* 3.3 39.6 - - - +
103T PHE 3.0 9.9 + - - -
104T TYR* 3.7 9.7 - - - -
130T GLU* 1.3 72.7 - - - +
132T LEU* 1.3 66.9 + - - +
133T LYS* 3.8 1.6 + - - +
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Residues in contact with LEU 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T LYS* 3.2 1.4 - - - -
103T PHE* 2.8 29.4 + - - -
129T SER* 3.7 21.5 - - - +
130T GLU 3.6 4.8 - - - +
131T GLY* 1.3 80.4 - - - +
133T LYS* 1.3 61.2 + - - +
134T SER* 4.0 6.1 - - - +
137T LEU* 4.1 27.6 - - + +
138T SER* 3.4 15.5 + - - +
141T LYS* 5.1 7.9 - - + -
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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