Contacts of the helix formed by residues 96 - 101 (chain A) in PDB entry 1FWZ
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 LYS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 20.6 - - + -
93A ASP* 2.7 35.1 + - + +
95A ASN* 1.3 85.9 - - - +
97A VAL* 1.3 66.5 + - - +
98A HIS 3.2 3.7 + - - -
99A ASP* 3.3 15.4 + - + +
100A GLU* 3.1 23.7 + - + +
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Residues in contact with VAL 97 (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* 3.6 39.9 - - + +
86A LEU* 3.9 9.6 - - + +
87A THR* 3.6 22.2 - - + -
92A LEU* 3.6 39.9 - - + +
93A ASP 3.3 5.3 + - - +
94A ILE* 3.5 12.0 + - - +
96A LYS* 1.3 76.9 - - - +
98A HIS* 1.3 56.4 + - - +
100A GLU* 3.9 1.0 - - - +
101A ALA* 3.0 27.5 + - - +
127A PRO* 4.8 0.2 - - + -
128A PHE* 4.2 10.1 - - + -
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.4 6.9 + - - -
17A GLU* 4.7 7.2 + - - -
79A HIS* 3.5 14.6 - + - -
83A GLU* 3.6 7.4 + - - +
94A ILE 4.7 1.0 + - - +
95A ASN 5.3 1.5 - - - +
96A LYS 3.3 1.0 - - - -
97A VAL* 1.3 74.6 - - - +
99A ASP* 1.3 70.2 + - - +
101A ALA* 3.2 2.8 + - - +
102A CSS 2.9 58.0 + - - -
128A PHE* 4.0 13.8 - + + -
301A ZN 1.8 37.5 - - - -
302A SO4 3.1 7.2 + - - -
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Residues in contact with ASP 99 (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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95A ASN 3.7 18.9 - - - +
96A LYS* 3.3 14.2 + - + +
98A HIS* 1.3 84.4 - - - +
100A GLU* 1.3 63.8 + - - +
102A CSS 3.3 21.8 + - - +
103A ARG* 3.7 19.1 + - - +
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Residues in contact with GLU 100 (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 LEU* 3.8 16.8 - - + -
92A LEU* 3.9 17.4 - - + +
96A LYS* 3.1 15.2 + - + +
97A VAL 3.9 3.6 - - - +
99A ASP* 1.3 79.1 - - - +
101A ALA* 1.3 58.0 + - - +
103A ARG* 3.0 43.7 + - - +
104A TRP* 2.8 57.4 + - + +
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Residues in contact with ALA 101 (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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79A HIS* 3.4 26.1 + - + +
82A ALA* 4.1 5.6 - - + -
83A GLU* 3.3 27.4 - - + +
86A LEU* 4.1 4.4 - - + +
97A VAL 3.0 20.5 + - - +
98A HIS 3.2 3.6 + - - +
100A GLU* 1.3 74.7 - - - +
102A CSS 1.3 57.6 + - - +
104A TRP* 4.0 9.1 - - - +
105A GLU* 3.0 27.5 + - - +
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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