Contacts of the strand formed by residues 106 - 110 (chain G) in PDB entry 3FKS
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 ASP 106 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G GLU 3.2 6.1 + - - +
73G LEU* 3.6 11.1 - - + +
74G ILE* 2.8 26.3 + - - +
105G ALA* 1.3 82.9 + - - +
107G ILE* 1.3 61.8 + - - +
108G VAL 4.2 0.4 - - - -
125G ASN* 3.6 8.4 - - - +
127G LYS* 3.2 34.3 + - + +
154G MET* 4.3 5.6 - - + -
159G TYR* 3.3 27.6 + - + +
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Residues in contact with ILE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ILE* 3.3 31.6 - - + +
76G ALA* 4.8 2.7 - - + -
95G VAL* 4.0 21.8 - - + -
99G LEU* 3.7 31.6 - - + -
106G ASP* 1.3 76.5 - - - +
108G VAL* 1.3 66.6 + - - +
109G THR* 3.7 22.9 - - + -
118G LEU* 3.9 17.3 - - + -
122G HIS* 5.6 1.1 - - + +
125G ASN* 2.9 26.5 + - + +
126G ILE* 3.2 24.7 - - + +
127G LYS* 3.2 7.3 + - - +
128G LEU 3.6 2.3 - - - +
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Residues in contact with VAL 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G LEU* 4.0 20.0 - - + -
74G ILE 2.7 12.1 + - - +
75G VAL* 3.3 9.5 - - + +
76G ALA* 2.8 31.9 + - - +
107G ILE* 1.3 74.8 - - - +
109G THR* 1.3 57.3 + - - +
110G ILE* 5.2 0.9 - - + -
128G LEU* 3.2 38.6 - - + +
130G ILE* 3.9 16.8 - - + -
146G ILE* 5.7 0.9 - - + -
150G LEU* 3.5 34.8 - - + -
154G MET* 4.2 10.5 - - + -
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Residues in contact with THR 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ALA* 4.0 5.6 - - + -
107G ILE* 3.7 9.9 - - + -
108G VAL* 1.3 75.5 - - - +
110G ILE* 1.3 58.2 + - - +
111G GLY 4.2 0.4 - - - -
114G ILE* 3.7 16.4 - - + -
115G LYS* 4.0 9.4 - - - +
118G LEU* 3.5 32.3 - - + -
126G ILE* 4.1 18.0 - - + +
128G LEU 2.9 9.0 + - - -
129G SER* 3.0 24.6 + - - -
130G ILE* 2.7 32.0 + - - -
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Residues in contact with ILE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G VAL* 4.2 11.2 - - + -
76G ALA 2.8 17.7 + - - +
77G ILE* 3.4 20.4 - - + -
78G THR 2.7 30.5 + - - +
108G VAL* 5.1 1.3 - - + +
109G THR* 1.3 71.8 - - - +
111G GLY* 1.3 58.2 + - - +
114G ILE* 3.6 5.2 - - - +
130G ILE* 4.0 32.1 - - + -
133G ILE* 4.4 7.0 - - + -
146G ILE* 3.8 19.3 - - + -
218G MET* 4.7 2.5 - - - -
222G MET* 3.4 32.1 - - + -
226G TYR* 3.8 20.6 - - - +
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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