Contacts of the strand formed by residues 116 - 125 (chain X) in PDB entry 2AT8
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 SER 116 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X TRP* 3.5 4.8 - - - -
111X TYR* 3.7 8.0 - - - -
112X ALA* 3.3 0.5 - - - -
113X ASP* 2.8 60.0 + - - +
115X SER* 1.3 76.1 - - - +
117X ALA* 1.3 65.3 + - - +
137X LEU 3.3 11.9 - - - -
138X ASN* 4.0 9.6 - - - -
146X GLY 6.2 0.4 - - - -
148X LYS* 4.9 1.0 - - - +
149X VAL* 4.0 20.7 + - - +
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Residues in contact with ALA 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X TYR* 4.0 27.8 - - + -
23X TRP* 4.1 4.7 - - + -
111X TYR* 3.1 16.4 - - - +
112X ALA* 4.1 3.1 - - + +
116X SER* 1.3 78.8 - - - +
118X LEU* 1.3 61.5 + - - +
119X ILE* 4.2 1.3 - - + -
135X ALA 4.5 0.2 - - - -
136X VAL* 3.4 4.3 - - - -
137X LEU* 2.8 46.4 + - + +
149X VAL* 3.6 9.2 - - - +
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Residues in contact with LEU 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110X MET* 2.8 56.5 + - + -
111X TYR* 2.8 21.5 + - + +
117X ALA* 1.3 73.2 - - - +
119X ILE* 1.4 70.2 + - - +
134X TYR* 4.6 4.9 - - + -
135X ALA 3.4 21.5 - - - +
136X VAL* 4.1 5.8 - - + -
149X VAL* 4.1 8.0 - - + +
152X ALA* 3.9 31.0 - - + +
153X VAL* 3.9 22.4 - - + +
156X ALA* 4.6 0.9 - - + -
158X LEU* 5.4 1.8 - - + -
163X PHE* 4.4 11.9 - - + -
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Residues in contact with ILE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X TYR* 3.8 12.3 - - + +
107X PHE* 3.7 42.6 - - + -
108X THR 3.2 13.2 - - - +
109X VAL* 4.1 11.7 - - + -
110X MET* 3.9 4.5 - - - -
117X ALA* 4.7 0.4 - - + -
118X LEU* 1.4 80.8 - - - +
120X HIS* 1.3 73.3 + - - +
121X THR* 4.1 7.6 - - + +
133X LEU 4.4 0.7 - - - +
134X TYR* 3.3 8.8 - - - +
135X ALA* 2.9 55.0 + - + +
137X LEU* 3.9 16.2 - - + -
185X FDD 4.0 12.6 - - + -
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Residues in contact with HIS 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X CYS* 5.6 0.2 - - + -
4X LYS* 3.9 17.0 + - + +
6X ALA* 3.6 28.5 - - + +
81X LYS* 5.7 1.3 + - - -
106X THR* 4.5 6.8 + - - -
107X PHE* 3.5 1.9 - - - -
108X THR* 2.9 36.4 + - - +
110X MET* 3.8 10.1 - - - -
119X ILE* 1.3 77.0 - - - +
121X THR* 1.3 83.1 + - - +
122X CYS* 4.0 11.2 - - + -
132X ASP* 2.8 36.4 + - + +
133X LEU 3.4 7.6 - - - -
134X TYR* 3.7 29.4 - + + -
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Residues in contact with THR 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X TYR* 3.6 19.6 - - - +
106X THR 2.8 20.2 + - - -
107X PHE* 4.3 7.0 - - - -
119X ILE* 4.2 10.1 - - + -
120X HIS* 1.3 83.0 - - - +
122X CYS* 1.3 61.2 + - - +
123X LEU* 4.1 1.1 + - - +
131X GLY 3.5 1.6 - - - +
133X LEU* 2.8 63.2 + - + +
185X FDD 4.0 22.3 - - + +
186X NO 4.2 4.5 - - - +
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Residues in contact with CYS 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X CYS* 2.0 52.9 - - + -
105X TYR* 3.2 2.9 - - - -
106X THR* 3.0 40.6 + - + +
120X HIS* 4.1 7.4 - - + -
121X THR* 1.3 76.0 + - - +
123X LEU* 1.3 63.0 + - - +
124X HIS* 3.2 34.3 - - - +
129X ASP* 4.4 0.2 - - - -
131X GLY 4.0 1.6 - - - -
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Residues in contact with LEU 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X PHE* 3.5 34.8 - - + -
104X TYR 3.9 2.7 - - - +
105X TYR* 3.9 8.5 - - + -
121X THR* 4.1 2.6 + - - +
122X CYS* 1.3 72.5 - - - +
124X HIS* 1.3 68.1 + - - +
125X LYS* 4.4 11.0 - - + -
128X LYS* 6.4 0.4 - - - -
129X ASP* 2.9 30.6 - - - +
130X LEU* 3.0 23.9 + - + +
131X GLY 4.5 4.6 + - - -
185X FDD 3.4 54.7 - - + -
186X NO 3.6 17.9 - - - +
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Residues in contact with HIS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X CYS* 5.6 1.3 - - + -
86X PHE* 3.8 4.9 - - - -
102X GLY 3.9 3.4 - - - +
103X ASN* 3.4 2.4 - - - -
104X TYR* 2.8 85.7 + + + +
106X THR* 5.1 3.2 - - + +
122X CYS* 3.2 38.7 - - + +
123X LEU* 1.3 75.1 - - - +
125X LYS* 1.3 61.9 + - - +
126X GLY 3.8 7.9 + - - +
128X LYS 3.3 7.6 + - - +
129X ASP* 4.1 13.7 - - + +
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Residues in contact with LYS 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X PHE* 3.7 19.7 - - + -
88X LYS* 5.1 5.7 - - - +
103X ASN* 3.4 16.8 - - - +
123X LEU* 4.3 12.5 - - + -
124X HIS* 1.3 73.1 - - - +
126X GLY* 1.3 63.2 + - - +
127X ASN 3.4 0.5 + - - -
128X LYS* 2.9 37.7 + - + +
129X ASP* 4.9 0.2 - - - +
185X FDD 2.9 63.3 + - + +
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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