Contacts of the strand formed by residues 85 - 89 (chain D) in PDB entry 1S89
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 VAL 85 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 5.5 0.9 - - + -
12D LYS* 4.3 20.6 - - + -
13D HIS 3.2 3.2 + - - -
14D ILE* 4.2 13.9 - - + -
15D ALA 2.8 25.9 + - - -
83D ILE* 3.3 9.3 - - - +
84D ASP* 1.3 86.3 - - + +
86D LEU* 1.3 63.9 + - - +
87D ILE* 4.1 24.0 - - + -
114D ILE* 4.5 1.1 - - - -
115D PRO* 3.7 27.6 - - + +
126D ILE* 4.6 5.4 - - + -
132D PHE* 4.0 29.4 - - + -
125E PHE* 6.0 0.7 - - + -
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Residues in contact with LEU 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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15D ALA* 3.7 22.0 - - + +
17D VAL* 4.4 11.2 - - + -
74D VAL* 4.5 7.6 - - + -
78D ILE* 4.2 4.3 - - + -
85D VAL* 1.3 75.5 - - - +
87D ILE* 1.3 76.9 + - - +
88D PHE* 4.1 18.6 - - + -
105D LEU* 4.1 25.1 - - + -
106D LEU* 4.7 4.7 - - + -
109D ALA* 3.9 23.3 - - + -
114D ILE* 4.1 14.5 - - + +
115D PRO 3.2 9.5 + - - +
116D VAL* 3.5 12.5 - - + -
117D ALA 2.9 25.3 + - - +
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Residues in contact with ILE 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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14D ILE* 4.3 9.4 - - + -
15D ALA 2.8 10.2 + - - +
16D LEU* 3.8 24.7 - - + -
17D VAL* 2.8 29.9 + - - +
26D LEU* 4.1 14.3 - - + +
29D TRP* 4.3 14.4 - - + -
85D VAL* 4.1 14.1 - - + -
86D LEU* 1.3 80.9 - - - +
88D PHE* 1.3 59.0 + - - +
89D PHE* 3.6 33.9 - - + -
117D ALA* 3.5 19.1 - - + +
123D ALA* 4.3 12.8 - - + +
126D ILE* 5.3 4.3 - - + -
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Residues in contact with PHE 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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17D VAL* 3.3 36.1 - - + -
18D ALA 4.7 0.2 - - - -
19D HIS* 4.0 7.9 - + - -
71D ASP* 4.4 2.5 - - - -
86D LEU* 3.8 15.4 - - + -
87D ILE* 1.3 74.7 - - - +
89D PHE* 1.3 60.3 + - - +
90D TRP* 3.1 26.1 + + + -
102D VAL* 3.7 47.1 - - + -
105D LEU* 3.7 28.3 - - + -
106D LEU* 4.0 23.8 - - + -
116D VAL* 5.7 0.2 - - + -
117D ALA 2.9 10.9 + - - +
118D THR* 3.3 19.4 - - + -
204D PGA 3.9 11.4 - - - -
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Residues in contact with PHE 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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17D VAL 2.8 8.3 + - - -
18D ALA* 3.4 8.2 - - + -
19D HIS 3.0 24.0 + - - -
22D CYS* 3.3 24.2 - - + +
25D MET* 4.2 6.1 - - + -
26D LEU* 3.8 45.5 - - + -
29D TRP* 4.5 6.5 - + + -
87D ILE* 3.6 25.6 - - + -
88D PHE* 1.3 75.0 - - - +
90D TRP* 1.3 59.8 + - - +
117D ALA 4.4 1.6 - - - -
118D THR 3.8 13.7 - - - -
119D ASN* 3.5 24.0 - - - -
120D VAL* 3.8 33.2 - - + -
123D ALA* 4.1 8.1 - - + -
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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