Contacts of the helix formed by residues 91 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.3 8.0 - - - +
90A ASN* 1.3 80.7 - - + +
92A HIS* 1.3 63.3 + - - +
93A HIS* 2.5 45.7 + - - +
94A HIS* 3.2 44.6 + - + +
95A ALA* 3.1 17.8 + - - +
410A LEU* 3.8 2.7 - - - -
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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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91A ASN* 1.3 75.5 + - - +
93A HIS* 1.3 104.1 + + - -
95A ALA* 3.6 7.5 - - + +
96A LYS* 3.1 32.9 + - - +
410A LEU* 3.9 16.2 - - + +
416A GLU* 3.9 36.2 + - + -
441A GLY* 3.6 28.1 + - - +
442A SER* 3.8 21.8 - - - -
444A LEU* 5.2 2.0 - - + -
434B ASP* 4.4 11.4 + - + -
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Residues in contact with HIS 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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91A ASN* 2.5 23.1 + - - +
92A HIS* 1.3 107.2 + + - +
94A HIS* 1.3 65.1 + - + +
96A LYS* 3.3 7.3 + - - +
97A GLU* 3.2 20.0 + - - +
346B LYS* 5.5 6.9 + - - -
434B ASP* 5.9 3.6 - - + -
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Residues in contact with HIS 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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89A VAL* 4.0 15.7 - - + +
91A ASN* 3.2 37.2 + - + +
93A HIS* 1.3 79.5 - - + +
95A ALA* 1.3 60.7 + - - +
97A GLU* 2.8 31.2 + - - +
98A ILE* 3.0 16.6 + - - +
392A VAL* 3.9 35.9 + - + +
393A GLY* 4.2 8.0 + - - -
395A TYR* 4.4 21.7 - + - -
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Residues in contact with ALA 95 (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 VAL* 3.8 7.8 - - + +
91A ASN 3.1 16.2 + - - +
92A HIS* 3.4 9.6 + - - +
94A HIS* 1.3 79.9 - - - +
96A LYS* 1.3 56.7 + - - +
98A ILE* 3.4 6.4 + - - +
99A LEU* 3.0 36.0 + - + +
405A ILE* 3.7 24.2 - - + -
410A LEU* 4.1 11.7 - - + -
444A LEU* 4.6 8.5 - - + -
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Residues in contact with LYS 96 (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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92A HIS* 3.1 24.4 + - - +
93A HIS* 3.9 4.9 - - - +
94A HIS 3.1 0.2 - - - -
95A ALA* 1.3 74.5 - - - +
97A GLU* 1.3 59.9 + - - +
98A ILE 3.3 0.4 - - - -
99A LEU* 4.5 2.0 - - + +
100A ILE* 3.2 29.1 + - + +
101A LYS* 3.1 22.5 + - - +
441A GLY* 2.5 41.6 + - - +
443A TYR 5.1 1.0 + - - -
444A LEU* 3.9 28.0 - - + +
448A ALA* 5.7 0.2 - - + -
346B LYS* 5.4 5.4 - - - +
359B GLY 3.9 20.7 + - - -
360B ASN* 4.0 18.8 + - - +
434B ASP 5.2 3.8 + - - -
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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 HIS 3.2 10.8 + - - +
94A HIS* 2.8 16.5 + - - +
96A LYS* 1.3 77.5 - - - +
98A ILE* 1.3 59.7 + - - +
101A LYS* 4.0 18.8 + - + -
102A LYS* 3.0 62.0 + - + +
106A PHE* 4.8 0.3 - - - -
391A SER* 3.2 11.1 + - - +
392A VAL* 3.5 17.2 - - + +
393A GLY* 3.3 23.4 + - - -
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Residues in contact with ILE 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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87A LEU* 5.5 1.3 - - + -
89A VAL* 5.0 4.9 - - + -
94A HIS 3.0 17.0 + - - +
95A ALA* 3.6 8.7 - - - +
97A GLU* 1.3 77.3 - - - +
99A LEU* 1.3 76.7 + - + +
102A LYS 3.0 23.9 - - - +
103A GLY* 3.2 3.8 - - - +
106A PHE* 3.4 42.4 - - + +
384A HIS* 4.6 6.0 + - + +
392A VAL* 3.6 37.0 - - + -
403A VAL* 4.2 25.4 - - + -
405A ILE* 4.5 6.7 - - + -
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Residues in contact with LEU 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 ALA 3.0 21.1 + - - +
96A LYS* 4.7 0.4 - - - -
98A ILE* 1.3 85.4 - - + +
100A ILE* 1.3 65.9 + - + +
103A GLY* 3.5 8.4 - - - -
381A LEU* 4.2 19.7 - - + -
384A HIS* 3.4 41.3 - - + +
405A ILE* 4.5 12.1 - - + -
444A LEU* 4.7 14.8 - - + -
447A GLY* 4.8 1.3 - - - -
448A ALA* 3.7 29.9 - - + +
449A GLY* 3.2 17.7 - - - -
450A VAL 3.3 9.2 + - - -
451A ARG 5.0 0.5 + - - -
600A HEM 3.7 7.9 - - - +
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Residues in contact with ILE 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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96A LYS* 3.2 39.7 + - + +
98A ILE 3.2 0.4 - - - -
99A LEU* 1.3 84.9 - - + +
101A LYS* 1.3 69.6 + - - +
102A LYS 3.1 1.1 - - - -
103A GLY* 3.2 9.6 + - - -
448A ALA* 3.9 18.8 - - + -
449A GLY* 3.6 19.3 - - - +
450A VAL* 5.1 3.6 - - - +
351B ARG* 4.9 0.9 + - - -
354B GLN* 5.7 2.3 + - - -
356B SER* 3.4 25.6 + - - +
357B ASP* 3.8 16.2 - - - +
359B GLY* 4.8 3.4 - - - +
360B ASN* 3.7 34.3 - - + +
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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