Contacts of the helix formed by residues 81 - 94 (chain D) in PDB entry 1H69
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 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LYS 4.2 6.5 + - - -
54D ASP* 2.8 31.8 + - - -
56D THR* 3.8 6.6 - - - +
79D HIS 3.8 0.4 + - - -
80D LEU* 1.3 73.9 - - - +
82D PRO* 1.3 76.1 - - - +
83D ASP* 2.5 24.1 + - - -
84D ILE* 2.9 22.3 + - - +
85D VAL* 3.2 7.6 + - - +
118D ARG* 4.4 3.4 + - - -
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Residues in contact with PRO 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D THR* 4.1 13.2 - - + -
80D LEU 3.3 6.0 - - - +
81D SER* 1.3 87.5 - - - +
83D ASP* 1.3 57.3 + - - +
85D VAL* 3.1 9.0 + - + +
86D ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 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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44D MET* 5.9 2.0 - - + +
46D PHE* 4.5 10.9 - - + -
47D ASN* 4.6 5.4 + - - +
81D SER* 2.5 32.4 + - - -
82D PRO* 1.3 75.4 - - - +
84D ILE* 1.3 64.1 + - - -
86D ALA* 3.8 7.0 + - - +
87D GLU* 3.4 25.8 + - - +
118D ARG* 2.4 32.7 + - - -
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Residues in contact with ILE 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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46D PHE* 5.7 0.9 - - + -
54D ASP* 3.8 23.3 - - + +
67D TYR* 4.2 2.7 - - - +
80D LEU* 4.0 19.3 - - + -
81D SER* 2.9 14.6 + - - +
83D ASP* 1.3 82.0 + - - +
85D VAL* 1.3 66.5 + - - +
87D GLU* 3.1 8.4 + - - +
88D GLN* 3.0 45.8 + - + +
118D ARG* 3.2 72.5 - - + +
119D VAL* 4.3 6.0 - - + +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR* 6.3 0.2 - - + -
78D GLY 6.3 1.1 - - - -
80D LEU* 3.7 29.4 - - + +
81D SER 3.7 10.8 - - - +
82D PRO* 3.1 10.6 + - + +
84D ILE* 1.3 76.5 - - - +
86D ALA* 1.3 63.3 + - - +
88D GLN* 2.9 18.4 + - + +
89D LYS* 2.9 49.6 + - + +
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Residues in contact with ALA 86 (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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82D PRO 2.9 16.0 + - - +
83D ASP* 4.0 8.5 - - - +
84D ILE 3.3 0.4 - - - -
85D VAL* 1.3 75.7 - - - +
87D GLU* 1.3 68.3 + - - +
89D LYS* 3.5 14.5 + - - +
90D LYS* 3.3 28.2 + - - +
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Residues in contact with GLU 87 (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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39D SER* 2.8 25.9 + - - -
44D MET* 3.2 19.2 - - + +
46D PHE* 4.4 6.3 - - + -
83D ASP 3.4 16.4 + - - +
84D ILE 3.1 7.7 + - - +
86D ALA* 1.3 76.2 - - - +
88D GLN* 1.3 65.0 + - - +
89D LYS 3.1 1.6 - - - -
90D LYS* 2.9 34.6 + - - +
91D LEU* 3.0 25.1 + - - +
115D TRP* 2.9 33.5 + - + +
119D VAL* 3.8 23.3 - - + -
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Residues in contact with GLN 88 (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 TYR* 3.7 13.0 - - - -
80D LEU* 3.5 17.5 - - - +
84D ILE* 3.0 31.8 + - + +
85D VAL* 2.9 16.5 + - + +
87D GLU* 1.3 76.9 - - - +
89D LYS* 1.3 58.0 + - + +
91D LEU* 3.3 1.4 + - - -
92D GLU* 3.0 27.5 + - - +
119D VAL* 3.0 28.4 + - + +
121D ILE* 3.7 13.9 - - - +
124D PHE* 3.4 48.9 - - + +
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Residues in contact with LYS 89 (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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85D VAL* 2.9 36.5 + - + +
86D ALA* 3.6 14.3 - - - +
88D GLN* 1.3 75.9 - - + +
90D LYS* 1.3 64.9 + - + +
92D GLU* 3.4 10.5 + - - +
93D ALA* 3.1 25.5 + - - +
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Residues in contact with LYS 90 (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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6D LEU* 3.9 25.3 - - + +
37D VAL* 4.1 17.9 - - + -
38D GLU 2.9 24.4 + - - +
39D SER* 3.0 19.1 + - - +
44D MET* 3.9 12.7 - - - +
86D ALA* 3.3 16.6 + - - +
87D GLU* 2.9 34.9 + - - +
89D LYS* 1.3 78.6 - - + +
91D LEU* 1.3 61.0 + - - +
93D ALA* 3.5 4.4 + - - +
94D ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 91 (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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6D LEU* 3.9 17.9 - - + -
87D GLU 3.0 11.8 + - - +
88D GLN 3.6 7.2 - - - +
89D LYS 3.2 0.4 - - - -
90D LYS* 1.3 76.8 - - - +
92D GLU* 1.3 59.3 + - - +
94D ALA* 3.1 11.4 + - - +
97D VAL* 4.0 20.2 - - + -
99D PHE* 5.5 0.4 - - + -
115D TRP* 4.0 14.8 - - + -
119D VAL* 3.7 21.8 - - + -
120D PHE* 3.4 29.4 - - + -
124D PHE* 3.9 18.2 - - + -
137D PHE* 4.1 10.1 - - + -
140D LYS* 2.8 26.8 + - + +
181D PHE* 4.4 13.0 - - + -
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Residues in contact with GLU 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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4D ARG* 5.2 0.2 + - - -
75D TYR* 4.0 7.1 + - - -
88D GLN 3.0 20.4 + - - +
89D LYS* 3.9 10.4 - - - +
91D LEU* 1.3 75.2 - - - +
93D ALA* 1.3 58.4 + - - +
124D PHE* 3.2 31.0 - - + -
137D PHE* 5.4 3.1 - - + -
140D LYS* 3.1 20.3 + - - +
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Residues in contact with ALA 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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4D ARG* 2.5 56.7 + - - +
89D LYS 3.1 17.1 + - - +
90D LYS* 4.0 4.9 - - - +
92D GLU* 1.3 77.2 - - - +
94D ALA* 1.3 59.2 + - - +
95D ASP* 4.0 0.9 + - - +
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Residues in contact with ALA 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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4D ARG* 4.1 5.2 - - - -
5D ALA 4.5 1.8 - - - -
6D LEU* 3.8 26.9 - - + +
90D LYS 3.1 17.2 + - - +
91D LEU 3.1 6.1 + - - +
93D ALA* 1.3 78.1 - - - +
95D ASP* 1.3 61.8 + - - +
96D LEU 3.9 9.9 - - - +
97D VAL* 4.1 8.3 - - + -
140D LYS* 2.8 35.2 + - - +
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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