Contacts of the strand formed by residues 107 - 112 (chain B) in PDB entry 2AFG
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 TRP 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 3.6 28.7 - - - -
69B THR 3.4 17.0 - - - -
70B ASP* 4.0 8.5 - - - -
71B GLY* 3.4 24.2 - - - -
98B ILE* 3.1 5.1 - - - +
99B SER* 2.9 28.6 + - - -
102B HIS* 3.4 43.3 + + + +
105B LYS* 3.1 45.9 + - + +
106B ASN* 1.3 77.1 - - - +
108B PHE* 1.3 59.9 + - - +
120B GLY* 3.6 16.2 - - - -
121B PRO* 3.4 31.0 - - + +
123B THR* 4.0 2.7 - - - -
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Residues in contact with PHE 108 (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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67B MET* 3.4 15.1 - - - +
88B ARG* 4.6 6.7 - - - -
96B THR* 4.2 10.5 - - - -
97B TYR 3.2 9.0 - - - +
98B ILE* 3.5 32.1 - - + -
106B ASN* 3.0 40.6 - - + -
107B TRP* 1.3 75.6 - - - +
109B VAL* 1.3 65.7 + - - +
110B GLY 3.6 1.7 + - - -
118B LYS 4.6 1.4 - - - +
120B GLY* 4.2 1.6 - - - -
123B THR* 3.1 27.3 + - - +
124B HIS* 4.4 2.0 - - - -
125B TYR* 4.0 33.0 - + + -
130B ILE* 3.4 47.8 - - + -
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Residues in contact with VAL 109 (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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14B LEU* 6.2 0.9 - - + -
23B LEU* 4.6 11.9 - - + -
56B ILE* 5.6 0.7 - - + -
65B LEU* 3.9 16.6 - - + -
67B MET* 4.5 2.0 - - + -
73B LEU* 3.9 24.5 - - + -
85B PHE* 3.3 42.0 - - + -
97B TYR* 3.0 26.9 + - + +
108B PHE* 1.3 80.5 - - - +
110B GLY* 1.3 61.0 + - - +
130B ILE* 3.9 6.1 - - - +
132B PHE* 3.3 30.0 - - + -
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Residues in contact with GLY 110 (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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73B LEU* 4.3 6.3 - - - +
108B PHE 3.6 3.8 + - - -
109B VAL* 1.3 80.6 - - - +
111B LEU* 1.3 65.6 + - - +
117B CYS* 3.7 5.4 - - - +
118B LYS* 2.8 34.6 + - - +
123B THR* 4.9 0.9 - - - -
129B ALA* 3.1 15.0 - - - -
130B ILE* 4.5 4.3 - - - -
132B PHE* 4.1 4.5 - - - -
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Residues in contact with LEU 111 (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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16B CYS* 4.0 25.9 - - + -
18B ASN* 2.9 23.7 + - - +
21B HIS* 4.4 11.0 - - + +
23B LEU* 4.1 31.2 - - + +
31B VAL* 5.5 1.1 - - + -
32B ASP* 4.0 14.6 - - - +
33B GLY* 4.2 17.3 - - - -
73B LEU* 5.7 0.9 - - + -
110B GLY* 1.3 77.0 - - - +
112B LYS* 1.3 64.7 + - - +
115B GLY* 3.6 22.0 - - - +
116B SER 3.6 6.5 - - - +
117B CYS* 3.9 14.1 - - + +
118B LYS* 4.4 0.9 - - - -
129B ALA* 3.1 17.6 + - - +
132B PHE* 4.3 6.0 - - + -
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Residues in contact with LYS 112 (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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18B ASN* 3.7 4.0 + - - +
21B HIS* 4.2 4.5 + - - -
110B GLY 4.2 0.6 + - - -
111B LEU* 1.3 78.7 - - - +
113B LYS* 1.3 63.4 + - - +
114B ASN* 2.9 25.9 + - - +
115B GLY* 3.1 10.4 + - - -
116B SER* 2.7 45.4 + - - +
117B CYS 3.5 18.9 + - - +
118B LYS* 3.9 18.6 - - + -
150B SO4 3.7 20.2 - - - +
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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