Contacts of the helix formed by residues 91 - 100 (chain B) in PDB entry 4R1Z
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 ASN 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.5 4.3 - - - +
90B ASN* 1.3 79.8 - - + +
92B HIS* 1.3 62.9 + - - +
93B HIS* 2.5 35.0 + - - +
94B HIS* 3.0 44.2 + - - +
95B ALA 3.0 18.7 + - - -
410B LEU* 3.7 4.0 - - - +
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Residues in contact with HIS 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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434A ASP* 3.6 23.1 - - - -
90B ASN 4.3 0.2 + - - -
91B ASN* 1.3 72.7 + - - +
93B HIS* 1.3 106.1 + + - +
95B ALA* 3.8 3.7 - - - +
96B LYS* 3.3 31.1 + - + +
410B LEU* 3.9 20.2 - - + +
416B GLU* 3.9 22.8 + - + -
441B GLY* 3.4 21.8 + - - +
442B SER* 3.6 31.6 + - - +
444B LEU* 5.6 1.6 - - + -
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Residues in contact with HIS 93 (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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346A LYS* 5.2 10.7 + - - +
434A ASP* 5.5 0.7 - - - -
91B ASN* 2.5 25.0 + - - +
92B HIS* 1.3 106.6 + + - +
94B HIS* 1.3 68.8 + - + +
96B LYS* 3.1 8.4 + - - +
97B GLU* 3.0 22.2 + - - +
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Residues in contact with HIS 94 (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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89B VAL* 3.8 18.1 - - + +
90B ASN 6.0 0.2 + - - -
91B ASN* 3.0 33.9 + - - +
93B HIS* 1.3 79.3 - - + +
95B ALA* 1.3 66.5 + - - +
97B GLU* 3.1 18.6 + - - +
98B ILE* 3.2 17.7 + - - +
392B VAL* 3.5 25.7 - - + +
393B GLY* 4.1 10.4 + - - -
394B GLU* 3.7 22.8 + - - -
395B TYR* 4.3 20.7 - + - -
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Residues in contact with ALA 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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89B VAL* 3.6 9.0 - - + +
91B ASN 3.0 13.6 + - - +
92B HIS 3.9 6.1 - - - +
94B HIS* 1.3 74.9 - - - +
96B LYS* 1.3 58.4 + - - +
98B ILE* 3.0 9.7 + - - +
99B LEU* 2.9 41.8 + - + +
405B ILE* 4.1 18.2 - - + -
410B LEU* 4.0 22.9 - - + -
444B LEU* 4.3 3.6 - - + -
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Residues in contact with LYS 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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346A LYS* 5.1 6.3 - - - +
359A GLY 3.7 21.3 - - - +
360A ASN* 3.3 27.1 + - - +
434A ASP 5.6 5.2 - - - -
92B HIS* 3.3 21.0 + - + +
93B HIS* 3.1 8.8 + - - +
95B ALA* 1.3 80.7 - - - +
97B GLU* 1.3 57.6 + - - +
99B LEU* 4.6 5.4 - - - +
100B ILE* 3.1 40.5 + - + +
101B LYS 3.3 3.1 + - - -
441B GLY* 2.7 39.8 + - - -
443B TYR 5.1 0.2 + - - -
444B LEU* 4.1 25.3 - - + +
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Residues in contact with GLU 97 (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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360A ASN* 5.8 0.2 - - - +
93B HIS 3.0 11.4 + - - +
94B HIS* 3.1 14.6 + - - +
96B LYS* 1.3 78.3 - - - +
98B ILE* 1.3 58.5 + - - +
101B LYS* 4.2 21.1 + - + -
102B LYS* 3.0 52.9 + - + +
391B SER 3.1 21.0 - - - +
392B VAL* 4.1 10.7 - - + +
393B GLY* 3.4 24.7 + - - -
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Residues in contact with ILE 98 (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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87B LEU* 4.8 2.7 - - + -
89B VAL* 4.8 4.5 - - + -
94B HIS 3.2 16.5 + - - +
95B ALA* 3.0 12.1 + - - +
97B GLU* 1.3 75.9 - - - +
99B LEU* 1.3 65.4 + - - +
102B LYS 3.2 23.6 - - - +
103B GLY* 3.3 3.3 - - - +
106B PHE* 3.5 37.9 - - + +
384B HIS* 4.5 9.5 + - + +
392B VAL* 3.1 37.7 - - + -
403B VAL* 4.2 27.6 - - + -
405B ILE* 4.3 14.4 - - + -
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Residues in contact with LEU 99 (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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95B ALA* 2.9 24.1 + - + +
96B LYS* 4.6 1.1 - - - +
98B ILE* 1.3 80.8 - - - +
100B ILE* 1.3 65.7 + - + +
103B GLY* 3.4 9.5 - - - -
381B LEU* 4.1 9.6 - - + -
384B HIS* 3.6 20.6 - - + +
405B ILE* 3.7 23.8 - - + -
444B LEU* 3.9 23.8 - - + -
447B GLY* 5.1 0.7 - - - -
448B ALA* 3.3 37.2 - - + +
450B VAL* 3.4 14.2 + - - +
451B ARG 4.9 0.9 + - - -
600B HEM 3.5 25.4 - - - +
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Residues in contact with ILE 100 (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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351A ARG* 4.2 1.4 + - - -
354A GLN* 5.6 0.9 - - - +
356A SER* 3.6 26.8 + - - +
357A ASP* 3.8 17.9 - - - +
359A GLY* 4.0 24.2 - - - +
360A ASN* 3.8 22.4 - - + +
96B LYS* 3.1 29.8 + - + +
99B LEU* 1.3 85.8 - - + +
101B LYS* 1.3 70.7 + - - +
102B LYS 2.9 2.7 + - - -
103B GLY* 2.9 10.2 + - - -
444B LEU* 5.7 0.2 - - + -
448B ALA* 3.9 19.5 - - + -
449B GLY* 3.8 16.6 - - - +
450B VAL* 5.2 1.3 - - - +
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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