Contacts of the helix formed by residues 71 - 85 (chain D) in PDB entry 1I94
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 SER 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A G 3.6 21.5 - - - -
530A A 5.5 6.5 - - - -
3D ARG* 4.1 19.2 - - - +
70D ILE* 1.3 75.3 - - - +
72D GLU* 1.3 56.5 + - - +
73D ARG* 2.6 24.6 + - - -
74D GLN* 2.9 8.3 + - - +
75D PHE* 2.8 20.0 + - - +
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Residues in contact with GLU 72 (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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528A C 4.0 35.0 - - - +
529A G 3.0 15.9 + - - +
65D ARG* 6.2 1.3 - - - -
70D ILE 3.5 2.8 + - - -
71D SER* 1.3 70.4 - - - +
73D ARG* 1.3 56.6 + - - +
75D PHE* 3.3 10.3 - - - +
76D ARG* 2.8 31.4 + - - +
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Residues in contact with ARG 73 (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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396A C 5.9 4.3 - - - +
397A G 5.6 4.7 - - - +
529A G 3.4 18.3 + - - +
71D SER* 2.6 7.5 + - - -
72D GLU* 1.3 75.6 - - - +
74D GLN* 1.3 67.4 + - - +
75D PHE 2.9 1.8 + - - -
76D ARG* 3.2 13.6 + - - +
77D ASN* 3.3 14.4 + - - +
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Residues in contact with GLN 74 (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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397A G 4.5 21.0 + - - +
398A C 6.2 0.2 - - - +
70D ILE* 4.5 13.2 - - + -
71D SER* 2.9 13.2 + - - +
73D ARG* 1.3 78.1 - - - +
75D PHE* 1.3 65.3 + - - +
77D ASN* 4.0 5.2 + - - +
78D LEU* 3.6 18.2 + - - +
137D SER* 6.1 4.9 - - - -
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Residues in contact with PHE 75 (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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65D ARG* 4.9 15.9 - - + -
70D ILE* 4.6 10.5 - - + +
71D SER 2.8 13.3 + - - +
72D GLU* 3.3 16.6 - - - +
74D GLN* 1.3 81.7 - - - +
76D ARG* 1.3 68.7 + - - +
78D LEU* 3.3 4.5 + - - +
79D PHE* 3.3 13.8 + - - +
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Residues in contact with ARG 76 (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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72D GLU 2.8 20.8 + - - +
73D ARG* 3.2 5.1 + - - +
75D PHE* 1.3 70.4 - - - +
77D ASN* 1.3 54.7 + - - +
78D LEU 2.6 0.9 + - - -
79D PHE* 2.4 43.7 + - - +
80D GLU* 3.0 4.4 + - - -
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Residues in contact with ASN 77 (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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396A C 5.3 10.1 - - - +
397A G 6.0 1.6 - - - +
73D ARG 3.3 11.5 + - - +
74D GLN* 4.4 6.1 - - - +
76D ARG* 1.3 77.2 - - - +
78D LEU* 1.3 55.7 + - - +
80D GLU* 3.4 10.7 + - - +
81D GLU* 2.9 24.3 + - - +
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Residues in contact with LEU 78 (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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74D GLN 3.6 9.4 + - - +
75D PHE* 3.3 9.5 + - - +
76D ARG 2.6 5.5 + - - -
77D ASN* 1.3 71.9 - - - +
79D PHE* 1.3 66.8 + - - +
80D GLU 3.1 1.3 - - - -
81D GLU* 3.0 10.8 + - + +
82D ALA* 2.8 24.5 + - - +
93D PHE* 5.4 4.1 - - - +
96D LEU* 5.3 14.6 - - + +
97D LEU* 5.9 3.4 - - - +
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Residues in contact with PHE 79 (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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75D PHE 3.3 7.1 + - - +
76D ARG* 2.4 31.0 + - - +
78D LEU* 1.3 73.0 - - - +
80D GLU* 1.3 61.4 + - - +
82D ALA* 3.0 10.6 - - - +
83D SER* 2.9 22.4 + - - -
93D PHE* 5.5 6.5 - - - -
207D TYR* 5.7 9.2 - - + -
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Residues in contact with GLU 80 (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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76D ARG 3.0 3.8 + - - +
77D ASN* 3.5 15.0 - - - +
79D PHE* 1.3 76.5 - - - +
81D GLU* 1.3 73.3 + - - +
82D ALA 2.8 1.4 + - - -
83D SER* 2.9 19.4 + - - -
84D LYS* 3.0 11.2 + - - +
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Residues in contact with GLU 81 (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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77D ASN 2.9 14.8 + - - +
78D LEU* 3.3 13.2 - - + +
80D GLU* 1.3 75.9 - - - +
82D ALA* 1.3 67.5 + - - +
84D LYS* 3.1 12.3 + - - +
85D LYS* 3.1 12.1 + - - +
96D LEU* 6.3 2.9 - - + -
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Residues in contact with ALA 82 (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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78D LEU 2.8 14.6 + - - +
79D PHE* 3.0 12.1 - - - +
80D GLU 2.8 0.8 + - - -
81D GLU* 1.3 69.1 - - - +
83D SER* 1.3 54.0 - - - +
84D LYS 2.2 18.5 + - - -
85D LYS* 2.4 32.0 + - - +
89D THR* 4.2 13.2 - - - +
92D VAL* 4.6 7.2 - - + -
93D PHE* 4.0 31.4 - - + +
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Residues in contact with SER 83 (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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5A U 5.0 14.6 - - - +
79D PHE 2.9 10.3 + - - -
80D GLU* 3.2 14.6 - - - -
82D ALA* 1.3 76.6 - - - +
84D LYS* 1.3 59.1 + - - -
85D LYS 4.0 5.2 - - - +
89D THR* 4.9 16.1 - - - -
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Residues in contact with LYS 84 (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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596A C 4.4 17.5 + - - +
80D GLU 3.0 5.5 + - - +
81D GLU* 3.3 11.4 - - - +
82D ALA 2.2 10.9 + - - -
83D SER* 1.3 73.3 - - - +
85D LYS* 1.3 63.5 + - - +
86D LYS 3.8 0.3 + - - -
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Residues in contact with LYS 85 (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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5A U 4.6 4.6 + - - +
596A C 5.4 2.9 - - - -
81D GLU 3.1 9.4 + - - +
82D ALA* 2.4 33.1 + - - +
83D SER 4.0 4.0 - - - +
84D LYS* 1.3 71.5 - - - +
86D LYS* 1.3 71.9 + - - +
87D GLY 3.5 9.0 + - - +
89D THR* 5.9 0.3 - - - -
92D VAL* 5.2 8.6 - - + +
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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