Contacts of the strand formed by residues 99 - 107 (chain B) in PDB entry 2ANL
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 PRO 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B SER* 5.4 5.4 - - - +
88B LYS* 4.2 25.2 - - + +
89B ASP 3.1 11.9 - - - +
90B LEU* 3.8 7.4 - - + -
98B LEU* 1.3 98.6 - - + +
100B TYR* 1.3 58.2 + - - +
142B GLU* 5.4 1.6 - - - +
146B GLN* 4.7 12.2 + - - +
148B LYS* 5.6 1.1 - - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN 6.2 0.7 - - - -
40B LEU* 4.4 22.9 - - + -
88B LYS* 3.1 12.1 - - - +
89B ASP 2.6 35.9 + - - +
91B VAL* 3.9 18.2 - - + -
98B LEU* 3.4 23.7 + - + -
99B PRO* 1.3 72.2 - - - +
101B LYS* 1.3 82.6 + - + +
102B PHE* 4.0 3.3 - - - -
124B LEU* 5.6 2.9 - - + -
136B ILE* 3.4 16.8 - - + +
137B ASP 2.3 33.8 + - - -
138B PRO* 3.6 1.6 - - - +
139B ILE* 2.9 39.2 + - + +
142B GLU* 3.9 18.6 - - + -
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 4.9 3.5 + - - +
69B ASP* 4.2 10.5 - - - +
86B PHE* 3.6 40.8 - - + -
87B SER 3.5 9.4 - - - +
88B LYS* 4.2 13.7 - - + +
100B TYR* 1.3 91.5 - - + +
102B PHE* 1.3 63.1 + - - +
134B GLY* 3.8 20.2 + - - -
135B SER 4.9 1.4 + - - -
136B ILE* 3.6 33.9 - - + +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 5.0 9.0 - - + -
40B LEU* 3.4 33.7 - - + +
42B VAL* 3.7 26.7 - - + -
58B TYR* 3.8 29.4 - + - -
86B PHE* 3.3 8.4 - - - -
87B SER* 2.9 53.7 + - - +
89B ASP* 3.6 28.9 - - + -
91B VAL* 4.6 11.2 - - + -
100B TYR 4.0 9.2 - - - -
101B LYS* 1.3 75.8 - - - +
103B ILE* 1.3 81.1 + - - +
104B GLU* 4.2 8.5 - - + -
136B ILE* 5.5 0.2 - - - -
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 4.5 6.5 - - - +
40B LEU 2.6 17.9 + - - +
41B TRP* 3.3 22.9 - - + +
42B VAL 3.3 7.4 + - - -
73B VAL* 3.3 30.3 - - + +
74B GLU* 5.4 0.2 - - - -
75B ILE* 4.0 31.6 - - + -
82B VAL* 6.2 3.4 - - + -
83B ARG 5.2 1.1 - - - -
84B GLY* 4.5 5.2 - - - +
85B PHE 3.8 14.1 - - - +
86B PHE* 3.7 22.4 - - + -
102B PHE* 1.3 82.7 - - - +
104B GLU* 1.3 72.9 + - - +
105B VAL* 4.1 11.4 - - + -
133B ILE* 5.9 0.7 - - + -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL 3.9 2.9 - - - +
44B SER* 2.7 32.6 + - - +
46B LYS* 4.0 8.8 + - - +
58B TYR* 3.8 26.1 - - + -
60B SER* 3.6 16.5 + - - -
66B TYR* 4.1 8.1 + - - -
84B GLY* 3.2 4.0 - - - -
85B PHE* 2.9 65.0 + - + +
87B SER* 2.6 26.1 + - - +
102B PHE* 4.0 5.7 + - + -
103B ILE* 1.3 69.9 - - - +
105B VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TRP* 3.1 53.8 - - + -
42B VAL 3.1 12.1 + - - +
43B PRO* 3.7 9.3 - - + +
44B SER* 2.7 34.6 + - - +
47B CYS* 3.6 3.3 - - - +
82B VAL* 4.3 23.6 - - + -
83B ARG 3.4 14.1 - - - +
84B GLY* 4.3 0.4 - - - -
103B ILE* 4.0 6.5 - - + +
104B GLU* 1.3 72.6 - - - +
106B THR* 1.3 69.7 + - - +
107B ASP 4.3 5.2 - - - +
108B THR* 4.9 6.1 - - + +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 5.0 0.3 - - - -
46B LYS* 3.5 21.1 + - - +
47B CYS* 2.5 38.2 - - - -
49B SER* 3.5 1.4 + - - -
83B ARG 2.8 11.6 + - - -
84B GLY* 4.2 7.0 - - - -
85B PHE* 3.5 23.5 - - - -
104B GLU 3.6 0.6 + - - -
105B VAL* 1.3 74.1 + - - +
107B ASP* 1.3 66.8 + - + +
108B THR* 3.5 0.7 + - - +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 3.9 3.4 + - - -
81B THR 4.4 0.3 - - - +
82B VAL* 3.8 3.6 - - - -
83B ARG* 3.1 56.4 + - + +
105B VAL* 4.6 2.2 - - - -
106B THR* 1.3 84.0 - - + +
108B THR* 1.3 69.3 + - - +
109B ASP* 3.3 19.8 - - - +
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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