Contacts of the strand formed by residues 120 - 130 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26L PHE* 4.0 12.8 - + - -
84L TRP 4.8 0.4 + - - -
85L ALA* 2.9 46.6 - - + +
86L HIS 3.1 28.6 + - - -
87L SER* 3.9 13.1 + - - -
112L ARG* 5.0 6.2 + - - -
114L GLN* 3.3 30.0 + - - +
112M ARG* 3.5 45.5 - - + +
113M VAL 3.2 14.6 - - - +
114M GLN* 4.2 1.1 - - - +
118M GLY 3.1 17.0 - - - -
119M SER* 1.3 78.0 - - - +
121M HIS* 1.3 71.2 + - - +
158M PHE* 4.7 3.3 - - - -
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Residues in contact with HIS 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ASN* 5.0 0.2 - - - -
81L TYR 4.5 3.6 - - - -
84L TRP* 3.3 52.9 + + - -
86L HIS* 2.8 41.3 - + + -
112M ARG* 4.5 1.8 - - - -
113M VAL* 2.8 38.4 + - + +
120M TYR* 1.3 84.9 + - - +
122M GLU* 1.3 60.8 + - - +
154M ALA* 3.8 11.0 - - - +
157M SER* 3.3 26.2 - - - -
158M PHE* 3.6 36.7 - + - -
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Residues in contact with GLU 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 3.0 31.0 + - - -
87L SER* 3.5 19.8 - - - -
88L ILE* 2.9 45.6 + - + +
147L VAL* 4.6 0.5 - - - +
89M THR* 2.6 38.3 + - - +
110M PHE* 3.7 7.1 - - - +
111M VAL 3.2 17.0 - - - +
112M ARG* 3.8 14.5 - - + +
121M HIS* 1.3 76.2 - - - +
123M ASP* 1.3 66.4 + - - +
154M ALA* 4.6 0.9 - - - -
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Residues in contact with ASP 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L HIS* 4.9 4.6 + - - +
88L ILE* 3.8 11.7 - - - -
147L VAL* 3.5 17.1 - - - +
148L THR* 5.1 2.9 + - - -
151L LEU* 6.2 0.2 - - - +
110M PHE* 3.5 3.6 - - - +
111M VAL* 3.0 32.7 + - - +
122M GLU* 1.3 76.1 - - - +
124M VAL* 1.3 70.2 + - - +
150M GLY* 4.5 1.9 - - - +
153M ARG* 2.3 53.9 + - + +
154M ALA* 3.7 23.6 - - + +
157M SER* 5.1 2.9 + - - -
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Residues in contact with VAL 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLN* 3.8 5.6 - - - +
143L ARG* 3.7 21.8 - - + +
144L LYS* 4.1 5.1 - - + -
147L VAL* 3.2 31.2 - - + -
108M CYS* 4.4 7.4 - - + -
109M ALA 3.2 7.2 - - - +
110M PHE* 3.1 38.6 - - + -
123M ASP* 1.3 86.5 + - - +
125M GLY* 1.3 66.9 + - - +
126M TYR* 6.1 0.4 - - + -
150M GLY* 4.0 2.7 - - - -
153M ARG* 2.8 33.3 + - - +
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Residues in contact with GLY 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L LYS* 4.5 1.8 - - - -
108M CYS* 3.3 7.4 - - - +
109M ALA 2.8 28.3 + - - -
124M VAL* 1.3 77.9 - - - +
126M TYR* 1.3 62.0 + - - +
146M ALA 3.5 7.6 - - - -
149M ASP* 3.4 7.2 - - - -
150M GLY* 3.4 27.7 - - - -
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Residues in contact with TYR 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L ALA* 3.7 15.0 - - - -
139L LEU* 3.3 17.4 - - + +
140L GLU* 3.6 44.8 - - + +
143L ARG* 3.7 18.2 - - + -
144L LYS* 4.0 4.5 - - + +
94M ASP* 2.6 40.1 + - - +
95M PHE* 4.0 2.3 - - - -
106M GLY* 3.5 22.7 - - - -
107M VAL 3.2 20.2 - - - -
108M CYS* 3.7 10.5 - - + -
124M VAL* 6.1 0.4 - - + -
125M GLY* 1.3 72.7 - - - -
127M GLY* 1.3 69.5 + - - +
128M VAL* 3.7 15.3 - - + -
145M GLU* 3.8 2.9 - - - +
146M ALA* 3.5 9.6 - - - -
149M ASP* 2.9 20.9 + - - +
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Residues in contact with GLY 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M GLY* 3.6 2.8 - - - -
107M VAL 2.7 36.2 + - - -
126M TYR* 1.3 75.4 - - - +
128M VAL* 1.3 66.0 + - - +
142M ALA* 3.3 29.2 - - - +
145M GLU* 4.1 7.0 - - - -
146M ALA* 3.6 5.5 - - - +
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Residues in contact with VAL 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L ALA* 3.6 30.5 - - + -
137L LEU* 4.7 7.9 - - + -
140L GLU* 4.8 11.9 - - - +
105M VAL 3.4 3.4 - - - +
126M TYR* 3.7 20.0 - - + -
127M GLY* 1.3 81.3 - - - +
129M SER* 1.3 63.0 + - - +
130M GLU* 3.8 23.1 - - + +
141M LYS* 2.7 34.4 + - - +
142M ALA* 4.2 3.5 - - - +
145M GLU* 3.7 7.2 + - - +
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Residues in contact with SER 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M PHE 3.5 3.3 - - - +
104M TYR* 3.5 1.9 - - - -
105M VAL* 2.8 39.0 + - - +
128M VAL* 1.3 79.7 - - - +
130M GLU* 1.3 60.8 + - - +
132M LEU* 3.6 15.6 - - - +
138M SER* 3.3 47.4 + - - -
141M LYS* 4.0 14.4 - - - +
142M ALA* 4.5 0.9 - - - -
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Residues in contact with GLU 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L SER* 2.8 30.3 + - - -
135L LYS 4.8 0.7 + - - -
136L ALA* 3.9 9.3 + - + +
137L LEU* 3.9 10.9 - - - +
103M PHE 3.5 2.9 - - - -
104M TYR* 3.6 32.0 - - + +
105M VAL 4.9 0.2 - - - +
128M VAL* 3.8 18.9 - - + +
129M SER* 1.3 79.3 + - - +
131M GLY* 1.3 61.0 + - - +
132M LEU* 3.6 5.7 + - - +
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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