Contacts of the helix formed by residues 91 - 96 (chain B) in PDB entry 4FDI
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 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 4.4 10.5 - - + +
90B ARG* 1.3 73.1 - - - +
92B PRO* 1.3 70.5 - - + +
93B ILE* 3.9 15.3 - - + -
94B ARG* 2.7 27.1 + - + +
95B ASN* 3.0 10.6 + - - -
343B MET* 3.4 24.0 - - + -
364B ASP* 2.8 36.1 + - - +
383B PHE* 4.4 22.4 - - + +
385B TYR* 4.1 24.7 - - + -
475B HIS* 3.7 25.8 - - + -
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Residues in contact with PRO 92 (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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75B ALA 3.9 14.4 - - - +
76B ASN* 3.4 26.7 - - - +
81B PRO* 3.5 25.4 - - + +
85B ALA* 4.1 11.4 - - + -
91B LEU* 1.3 88.5 - - + +
93B ILE* 1.3 56.7 + - - +
95B ASN* 3.4 13.0 - - - +
96B GLY* 2.9 27.7 + - - -
97B PHE 3.2 28.2 + - - +
98B TYR* 3.6 8.3 - - + -
385B TYR* 5.9 2.7 - - + -
387B GLY 6.0 0.9 - - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.1 19.2 - - + -
92B PRO* 1.3 77.9 - - - +
94B ARG* 1.3 60.4 + - + +
98B TYR* 3.7 40.2 - - + +
385B TYR* 4.0 38.1 - - + +
387B GLY 4.5 2.8 + - - +
388B ASP* 4.2 18.6 - - + +
475B HIS* 5.2 0.7 - - + +
479B LEU* 4.0 27.1 - - + -
481B PRO* 3.6 20.5 - - + +
482B ALA* 3.0 26.0 + - - +
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.2 38.8 + - + +
91B LEU* 2.7 18.3 + - + +
93B ILE* 1.3 76.0 - - + +
95B ASN* 1.3 57.6 + - - +
96B GLY 3.3 2.2 - - - -
121B GLU* 3.5 2.3 - - - +
362B ALA* 3.5 34.8 - - - +
363B ILE 5.9 0.2 - - - -
364B ASP* 2.8 40.7 + - - +
475B HIS* 3.4 28.5 + - - -
478B ALA* 4.8 4.4 + - - +
479B LEU* 3.4 43.2 - - + +
480B VAL 5.5 2.2 - - - +
482B ALA* 3.1 20.4 - - - +
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Residues in contact with ASN 95 (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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81B PRO 4.4 0.2 + - - -
84B ALA* 3.7 9.3 - - + +
85B ALA 3.6 14.5 - - - +
88B THR* 3.4 16.3 + - + +
90B ARG* 2.9 28.0 + - + +
91B LEU 3.0 13.5 + - - +
92B PRO* 3.4 5.1 - - - +
94B ARG* 1.3 77.1 - - - +
96B GLY* 1.3 57.1 + - - +
97B PHE* 3.0 32.6 + - - +
117B ILE* 4.9 1.3 - - + -
118B PRO* 3.6 27.1 - - - +
121B GLU* 3.4 27.6 - - + +
482B ALA* 4.5 1.3 - - - -
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Residues in contact with GLY 96 (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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92B PRO 2.9 7.2 + - - -
94B ARG 3.3 4.0 + - - -
95B ASN* 1.3 78.1 - - - +
97B PHE* 1.3 59.2 + - - +
98B TYR* 2.9 16.3 + - - +
118B PRO* 5.7 0.4 - - - -
482B ALA* 3.9 7.8 - - - +
483B GLN 3.8 18.4 - - - -
484B PRO* 3.7 0.3 - - - +
485B GLN* 2.8 36.0 + - - +
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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