Contacts of the helix formed by residues 96 - 105 (chain A) in PDB entry 4K71
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 PRO 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A HIS* 6.0 4.0 - - - +
95A GLU* 1.3 87.9 - - + +
97A GLU* 1.3 83.0 + - - +
98A ARG 3.2 3.4 + - - -
99A ASN* 3.2 13.5 + - + +
100A GLU* 3.2 20.4 + - + +
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Residues in contact with GLU 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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93A LYS* 4.4 20.0 + - + +
94A GLN* 3.2 13.8 + - - +
95A GLU 3.6 2.3 - - - +
96A PRO* 1.3 99.1 - - - +
98A ARG* 1.3 58.2 + - - +
100A GLU* 3.3 9.9 + - - +
101A CYS* 2.9 28.6 + - - +
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Residues in contact with ARG 98 (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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68A THR* 3.2 27.7 + - - +
71A GLY* 3.4 16.8 + - - -
72A ASP* 3.2 22.4 + - - +
75A CYS* 4.0 20.7 - - - +
90A CYS* 3.4 24.3 - - - +
91A CYS* 4.6 1.8 + - - +
93A LYS* 3.7 18.7 + - - +
94A GLN* 2.9 18.9 + - - +
95A GLU* 2.6 38.9 + - - +
96A PRO 3.2 0.2 - - - -
97A GLU* 1.3 77.6 - - - +
99A ASN* 1.3 61.7 + - - +
101A CYS* 3.2 5.5 + - - +
102A PHE* 3.1 36.0 + - + -
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Residues in contact with ASN 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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30A TYR* 2.9 30.7 + - - -
67A HIS* 3.1 46.6 + - + +
95A GLU* 3.1 23.1 + - - +
96A PRO* 3.2 4.8 + - + +
98A ARG* 1.3 78.6 - - - +
100A GLU* 1.3 64.8 + - + +
102A PHE* 3.3 12.9 + - - +
103A LEU* 3.1 38.6 + - - +
247A HIS* 4.2 4.9 + - - -
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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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67A HIS* 5.9 0.2 - - - -
96A PRO* 3.2 17.8 + - + +
97A GLU* 3.5 11.4 - - - +
99A ASN* 1.3 78.3 + - + +
101A CYS* 1.3 61.1 + - - +
103A LEU* 3.5 10.9 + - - +
104A GLN* 3.3 38.7 + - - +
247A HIS* 3.0 32.3 + - - -
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Residues in contact with CYS 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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89A ASP* 4.2 5.2 - - - -
90A CYS* 2.1 54.7 - - + -
93A LYS* 4.3 19.3 - - + +
97A GLU 2.9 12.8 + - - +
98A ARG 3.2 7.8 + - - +
100A GLU* 1.3 74.1 - - - +
102A PHE* 1.3 62.6 + - - +
104A GLN* 3.3 15.0 + - - +
105A HIS* 2.8 40.4 + - - -
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Residues in contact with PHE 102 (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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30A TYR* 3.7 26.9 - + + +
31A LEU* 6.0 1.8 - - + -
71A GLY* 4.2 16.2 - - - -
74A LEU* 4.3 23.6 - - + -
75A CYS* 3.8 24.7 - - - -
78A ALA* 5.0 4.5 - - + -
87A MET* 3.9 26.1 - - - +
90A CYS* 3.3 26.0 - - + -
91A CYS* 4.2 4.0 - - - -
95A GLU* 4.9 0.2 - - - -
98A ARG* 3.1 41.1 + - + -
99A ASN* 3.3 18.8 + - + +
101A CYS* 1.3 75.7 - - - +
103A LEU* 1.3 62.6 + - - +
105A HIS* 3.0 13.7 + - - +
106A LYS* 3.5 12.1 + - - +
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Residues in contact with LEU 103 (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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30A TYR* 3.8 21.8 - - + +
99A ASN* 3.1 24.0 + - - +
100A GLU* 3.7 17.9 - - - +
101A CYS 3.3 0.4 - - - -
102A PHE* 1.3 81.1 - - - +
104A GLN* 1.3 60.3 + - + +
105A HIS 3.5 0.3 + - - -
106A LYS* 3.7 29.4 + - + +
148A TYR* 4.0 9.7 + - - -
246A CYS 5.1 2.7 - - - +
247A HIS* 3.4 62.4 - - + +
248A GLY* 4.2 3.6 - - - +
466A LYS* 5.8 0.2 + - - -
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Residues in contact with GLN 104 (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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100A GLU* 3.3 27.7 + - - +
101A CYS* 3.7 11.1 - - - +
102A PHE 3.2 0.8 - - - -
103A LEU* 1.3 75.4 - - + +
105A HIS* 1.3 72.5 + - + +
106A LYS 3.5 1.3 + - - -
466A LYS* 3.7 29.7 + - - +
146B LYS* 5.2 7.8 + - - -
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Residues in contact with HIS 105 (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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32A GLN* 4.2 0.5 - - - +
86A GLU* 3.6 41.2 - - + +
87A MET* 3.4 36.9 - - + +
89A ASP* 5.4 1.3 - - + -
90A CYS* 3.5 8.8 - - - -
101A CYS* 2.8 40.7 + - - +
102A PHE 3.0 4.1 + - - +
104A GLN* 1.3 89.5 + - + +
106A LYS* 1.3 66.8 + - - +
107A ASP* 3.0 8.7 + - - +
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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