Contacts of the strand formed by residues 73 - 77 (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 LEU 73 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G GLU* 1.3 71.3 - - - +
74G ILE* 1.3 63.7 + - - +
75G VAL* 4.8 4.4 - - + +
106G ASP* 3.7 14.4 - - + +
108G VAL* 4.0 11.7 - - + -
150G LEU* 3.7 35.0 - - + -
154G MET* 3.8 20.0 - - + -
156G ALA* 3.7 24.7 - - + -
159G TYR* 3.3 30.2 - - + +
161G LYS 3.0 8.9 + - - +
162G ILE* 3.6 21.4 - - + +
163G SER* 2.9 28.2 + - - +
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Residues in contact with ILE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 3.6 29.4 - - + +
73G LEU* 1.3 75.0 - - - +
75G VAL* 1.3 64.2 + - - +
76G ALA 4.9 0.4 - - - +
95G VAL* 4.3 11.2 - - + -
98G HIS* 4.8 4.7 - - + -
99G LEU* 3.6 34.1 - - + -
105G ALA* 4.1 3.4 - - + -
106G ASP 2.8 12.0 + - - +
107G ILE* 3.3 27.1 - - + -
108G VAL* 2.7 33.6 + - - +
163G SER* 3.6 4.0 - - - -
165G PHE* 3.5 35.2 - - + -
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU* 4.8 8.3 - - + +
74G ILE* 1.3 80.1 - - - +
76G ALA* 1.3 62.0 + - - +
77G ILE* 3.6 23.7 - - + +
108G VAL* 3.3 11.9 - - + +
110G ILE* 4.2 9.2 - - + -
150G LEU* 4.4 19.1 - - + -
162G ILE* 5.0 4.5 - - + -
163G SER 2.9 16.2 + - - +
164G ILE* 3.8 14.1 - - + -
165G PHE* 2.8 31.2 + - - +
218G MET* 3.8 29.8 - - + -
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Residues in contact with ALA 76 (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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74G ILE* 4.1 1.2 + - - +
75G VAL* 1.3 72.4 - - - +
77G ILE* 1.3 63.7 + - - +
78G THR 4.0 0.4 - - - -
91G LEU* 5.9 0.7 - - + -
95G VAL* 5.1 8.3 - - + -
107G ILE* 4.8 2.7 - - + -
108G VAL 2.8 15.5 + - - +
109G THR* 4.0 15.7 - - + -
110G ILE* 2.8 32.0 + - - +
114G ILE* 3.6 28.7 - - + -
118G LEU* 4.4 6.7 - - + -
165G PHE* 4.1 6.1 - - - -
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Residues in contact with ILE 77 (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* 3.6 15.0 - - + +
76G ALA* 1.3 76.5 - - - +
78G THR* 1.3 74.7 + - - +
91G LEU* 3.3 12.8 - - - +
110G ILE* 3.4 31.0 - - + -
164G ILE* 3.8 20.2 - - + -
165G PHE 3.0 22.9 + - - +
166G TYR* 4.1 7.8 - - + -
167G ASN* 4.0 4.9 + - - -
218G MET* 5.3 5.4 - - + -
221G ALA* 4.3 8.3 - - + +
222G MET* 3.8 39.0 - - + +
225G GLY* 5.3 4.3 - - - -
226G TYR* 4.6 9.4 - - + +
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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