Contacts of the strand formed by residues 87 - 92 (chain F) in PDB entry 6S1M
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 ILE 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F ARG* 3.7 52.3 - - + +
6F LEU 3.8 10.8 - - - +
7F VAL* 4.1 29.4 - - + +
85F GLU 4.8 3.1 - - - +
86F ASP* 1.3 72.9 - - - +
88F ILE* 1.3 63.8 + - - +
89F THR* 4.5 1.2 + - - +
102F VAL 3.4 2.3 - - - +
103F PHE* 3.3 2.8 - - - -
104F GLU* 2.7 48.9 + - + +
106F PRO* 5.8 7.6 - - + -
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 3.7 0.3 - - - -
6F LEU* 2.8 41.7 + - + +
9F GLY* 3.3 37.7 - - - +
12F LEU* 4.0 24.0 - - + -
13F LYS* 4.6 2.5 - - + -
79F LEU* 4.1 19.5 - - + -
82F ALA* 4.3 11.9 - - + -
83F GLY 5.6 0.7 - - - +
86F ASP 4.2 6.3 - - - +
87F ILE* 1.3 72.8 - - - +
89F THR* 1.3 71.3 + - - +
90F LEU* 4.2 9.4 - - + -
101F LEU* 5.0 0.7 - - + -
102F VAL 3.4 2.9 - - - +
103F PHE* 3.5 31.6 - - + -
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLU* 4.3 20.0 - - + +
4F ALA 3.2 15.5 - - - +
5F ARG* 3.7 26.4 + - + +
87F ILE* 4.5 1.9 + - - +
88F ILE* 1.3 80.5 + - - +
90F LEU* 1.3 70.3 + - - +
91F ARG* 4.6 8.8 - - + +
100F ALA 3.1 13.3 - - - +
101F LEU* 3.7 0.7 - - - -
102F VAL* 2.8 38.5 + - + +
104F GLU* 4.1 7.3 + - - -
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PHE* 3.5 32.5 - - + -
3F GLU* 3.3 1.6 - - - -
4F ALA* 2.8 36.7 + - + +
12F LEU* 3.6 33.7 - - + -
28F TRP* 5.5 7.9 - - + -
30F ILE* 5.8 1.3 - - + -
35F VAL* 4.9 11.2 - - + -
52F LEU* 6.4 1.1 - - + -
57F PHE* 5.2 10.8 - - + -
75F MET* 4.8 9.6 - - + -
88F ILE* 4.2 4.2 - - + -
89F THR* 1.3 77.1 - - - +
91F ARG* 1.3 60.5 + - - +
99F LEU* 4.5 13.5 - - + -
100F ALA 3.5 2.9 - - - +
101F LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 5.4 3.8 - - + -
2F PHE 3.2 14.8 - - - +
3F GLU* 2.9 33.1 + - - +
89F THR* 4.6 9.3 - - + +
90F LEU* 1.3 76.4 - - - +
92F ALA* 1.3 64.7 + - - +
93F GLU* 4.6 9.2 - - - +
98F THR 4.8 0.3 - - - +
99F LEU* 3.7 3.3 - - - +
100F ALA* 2.9 47.0 + - + +
102F VAL* 3.7 28.7 - - + +
113F ASP* 4.3 6.9 + - - -
115F GLU* 5.2 1.2 + - - -
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.6 0.7 - - - +
2F PHE* 2.8 45.5 + - + +
66F LEU* 5.5 4.7 - - + -
68F MET* 4.3 20.6 - - + -
91F ARG* 1.3 76.5 - - - +
93F GLU* 1.3 81.7 + - - +
96F ALA 5.8 0.2 - - - +
98F THR 4.4 7.4 - - - +
99F LEU* 3.8 15.0 - - + -
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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