Contacts of the helix formed by residues 91 - 100 (chain D) in PDB entry 1I43
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 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378B ASP* 3.6 21.8 - - + +
385B ILE* 4.0 7.2 - - - -
89D PHE* 3.3 3.0 - - - +
90D ASN* 1.3 84.3 - - - +
92D THR* 1.3 67.8 + - - +
93D SER* 4.1 19.3 - - - +
94D GLU* 2.8 40.4 + - + +
95D LEU* 3.1 10.3 + - - +
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ALA* 3.6 24.6 - - + +
377B VAL* 3.1 19.6 - - - +
378B ASP* 2.7 29.8 + - - -
385B ILE* 4.1 5.0 - - - +
398B GLN* 4.0 2.5 + - - +
401B ILE* 3.4 32.8 - - + -
91D LYS* 1.3 70.7 - - - +
93D SER* 1.3 61.3 + - - +
95D LEU* 3.2 14.2 + - + +
96D ILE* 3.0 29.6 + - + +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ASP* 4.4 2.9 + - - -
91D LYS* 2.9 21.8 + - - +
92D THR* 1.3 77.8 - - - +
94D GLU* 1.3 61.7 + - - +
96D ILE* 3.3 14.9 + - - +
97D ASP* 3.1 34.2 + - - +
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE* 4.4 7.7 - - + -
90D ASN* 3.2 44.8 + - - +
91D LYS* 2.8 30.0 + - + +
93D SER* 1.3 77.6 + - - +
95D LEU* 1.3 67.4 + - - +
96D ILE 3.1 0.2 - - - -
97D ASP* 3.0 21.5 + - - +
98D PHE* 3.0 14.6 + - - +
103D ARG* 3.6 43.3 + - - +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ILE* 4.5 14.1 - - + -
398B GLN* 5.4 4.7 - - + +
401B ILE* 3.7 25.6 - - + -
402B MET* 3.9 35.2 - - + +
89D PHE* 3.6 43.8 - - + -
91D LYS 3.1 8.7 + - - +
92D THR* 3.4 18.4 - - + +
94D GLU* 1.3 77.2 - - - +
96D ILE* 1.3 62.8 + - - +
98D PHE* 3.4 3.5 + - + +
99D LYS* 3.1 31.2 + - + +
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 4.9 12.3 - - + -
371B LEU* 6.1 2.5 - - + -
401B ILE* 3.9 23.6 - - + -
405B TRP* 3.8 21.3 - - + +
92D THR* 3.0 29.9 + - + +
93D SER* 3.4 10.5 - - - +
95D LEU* 1.3 74.9 - - - +
97D ASP* 1.3 66.4 + - - +
99D LYS* 3.0 6.9 + - - +
100D GLU* 2.8 49.8 + - + +
102D ARG* 4.4 4.9 - - - +
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D SER* 3.1 24.7 + - - +
94D GLU* 3.0 17.1 + - - +
96D ILE* 1.3 76.4 - - - +
98D PHE* 1.3 56.8 + - - +
100D GLU 3.1 8.0 + - - -
101D LYS 3.2 0.2 + - - -
102D ARG* 2.8 67.1 + - + +
103D ARG* 3.9 21.9 + - + +
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.9 21.8 - + + -
94D GLU 3.0 11.4 + - - +
95D LEU* 3.7 10.3 - - + +
97D ASP* 1.3 76.3 - - - +
99D LYS* 1.3 82.5 + - + +
101D LYS* 3.1 15.8 + - - +
103D ARG* 3.6 31.8 - - + +
105D SER* 3.1 38.4 - - - -
106D PHE 5.0 0.2 - - - -
107D GLU* 3.5 43.1 - - + -
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Residues in contact with LYS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ILE* 3.8 20.2 + - + +
402B MET* 2.7 30.3 + - - -
403B SER* 4.4 4.9 - - - +
404B TYR 5.5 0.2 - - - +
405B TRP* 3.6 28.4 - - + +
601B PMC 4.8 1.4 + - - -
95D LEU* 3.1 27.3 + - + +
96D ILE* 3.0 10.6 + - - +
98D PHE* 1.3 89.0 - - + +
100D GLU* 1.3 57.9 + - - +
101D LYS* 3.3 12.3 + - - +
107D GLU* 3.0 26.3 + - - -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B TRP* 3.1 24.0 + - + +
96D ILE* 2.8 37.1 + - + +
97D ASP 3.1 3.3 + - - +
99D LYS* 1.3 80.5 - - - +
101D LYS* 1.3 71.0 + - - +
102D ARG* 2.7 49.8 + - - +
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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