Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 3FCL
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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU 5.5 0.7 - - - -
84A PHE 4.2 0.8 - - - -
85A PHE* 1.3 75.8 - - - +
87A GLU* 1.3 60.4 + - - -
88A SER 3.4 2.7 - - - -
89A TRP* 3.3 6.8 + - - +
90A LYS* 3.0 22.0 + - - +
129A THR* 2.9 35.3 + - - -
130A GLN* 4.5 6.2 - - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 4.7 3.8 - - - +
85A PHE 3.5 2.1 + - - +
86A GLY* 1.3 69.6 - - - -
88A SER* 1.3 60.1 + - - +
90A LYS* 3.1 41.0 + - - +
91A LYS* 3.0 32.6 + - + +
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.4 0.4 - - - -
87A GLU* 1.3 77.9 - - - +
89A TRP* 1.3 69.3 + - - +
91A LYS* 3.7 11.1 + - - +
92A HIS* 3.5 25.3 - - - -
133A ASP* 3.4 34.5 + - - -
134A ILE* 3.1 23.9 + - - +
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.8 14.8 - - + -
86A GLY* 3.5 9.0 - - - +
87A GLU 3.3 0.2 - - - -
88A SER* 1.3 85.7 + - - +
90A LYS* 1.3 59.1 + - - +
92A HIS* 3.1 3.8 + - - +
93A LEU* 2.9 39.9 + - + +
128A TRP* 3.7 36.3 - + - -
129A THR* 3.1 34.1 + - + -
132A CYS* 2.9 29.2 + - - -
134A ILE* 3.5 44.2 - - + +
137A VAL* 3.7 26.2 - - + -
201A LEU* 3.9 22.0 - - + -
229A VAL* 4.2 13.2 - - + -
233A LEU* 4.9 2.5 - - + -
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.9 17.0 + - - -
85A PHE* 3.5 35.1 + - + +
86A GLY 3.0 11.8 + - - +
87A GLU* 3.1 38.9 + - - +
89A TRP* 1.3 77.4 - - - +
91A LYS* 1.3 63.0 + - - +
93A LEU 4.4 0.4 - - - +
94A SER* 2.9 36.5 + - - +
97A PHE* 3.9 21.1 - - + -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.0 21.2 + - + +
88A SER* 3.7 10.5 - - - +
89A TRP 3.2 0.2 - - - -
90A LYS* 1.3 76.6 - - - +
92A HIS* 1.3 82.5 + - + +
94A SER* 3.8 10.2 + - - -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A SER 3.5 19.5 + - - +
89A TRP 3.1 6.7 + - - +
91A LYS* 1.3 103.6 + - + +
93A LEU* 1.3 60.9 + - + +
94A SER 3.6 0.4 - - - -
95A GLY 5.0 1.9 + - - -
134A ILE* 3.7 21.3 - - + +
135A LYS* 4.4 11.5 - - + +
232A TRP* 3.4 62.0 + + + +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 4.1 17.7 - - + -
89A TRP* 2.9 40.4 + - + +
92A HIS* 1.3 81.9 - - + +
94A SER* 1.3 65.5 + - - +
95A GLY 3.1 3.4 - - - -
96A GLU* 3.0 26.3 + - + +
97A PHE* 4.0 15.9 - - + -
128A TRP* 4.5 2.0 - - + -
134A ILE* 5.1 3.8 - - + -
225A PHE* 4.3 10.8 - - + -
228A ALA* 4.2 11.0 - - + +
229A VAL* 3.9 46.7 - - + +
232A TRP* 4.7 9.4 - - + -
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 2.9 23.1 + - - -
91A LYS* 3.8 10.0 + - - -
92A HIS 3.6 0.8 - - - -
93A LEU* 1.3 75.9 - - - +
95A GLY* 1.3 63.3 + - - +
96A GLU 3.1 0.2 - - - -
97A PHE* 3.1 38.2 + - - +
98A GLY 4.3 1.9 + - - -
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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