Contacts of the strand formed by residues 97 - 102 (chain X) in PDB entry 2OTT
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 97 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X THR* 4.3 13.2 - - + -
34X ALA* 3.6 27.1 - - + +
35X LEU 3.6 7.0 - - - +
64X VAL* 3.5 4.2 - - - +
65X LEU* 3.0 39.5 + - + -
66X ASP* 3.3 21.5 - - - +
72X SER* 3.1 25.7 - - - +
73X ARG 3.4 24.3 + - - +
95X CYS* 3.4 8.3 + - - +
96X LYS* 1.3 77.2 - - - +
98X VAL* 1.3 68.8 + - - +
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Residues in contact with VAL 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23X THR* 3.2 3.9 - - - +
24X VAL* 2.8 34.9 + - + +
35X LEU* 4.2 6.6 + - + +
37X ASP* 3.7 30.5 - - + +
47X TRP* 3.8 30.1 - - + -
62X TYR* 4.1 9.4 - - + -
63X ARG 3.6 10.5 - - - +
64X VAL* 5.1 8.1 - - + -
65X LEU* 4.0 4.0 - - - -
96X LYS* 4.4 0.7 - - + +
97X LYS* 1.3 85.3 - - - +
99X PHE* 1.3 65.7 + - - +
100X VAL* 3.8 19.1 - - + -
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Residues in contact with PHE 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X VAL 5.5 0.4 - - - -
15X GLY 5.5 2.2 - - - -
16X GLY* 5.1 6.1 - - - -
21X GLU* 4.0 19.7 - - + -
22X GLY* 3.4 29.8 - - - -
23X THR* 4.1 10.1 - - - +
62X TYR* 2.9 26.2 - - - +
63X ARG* 2.9 59.8 + - + +
65X LEU* 3.9 15.8 - - + +
98X VAL* 1.3 71.5 - - - +
100X VAL* 1.3 69.7 + - - +
101X THR* 3.6 25.1 - - + -
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Residues in contact with VAL 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 4.0 14.4 - - + +
21X GLU* 3.2 4.0 - - - -
22X GLY 2.9 31.3 + - - -
24X VAL* 3.6 22.2 - - + -
47X TRP* 3.9 23.6 - - + +
50X VAL* 5.3 2.0 - - + -
51X CYS* 3.6 31.0 - - - -
59X VAL* 3.9 13.9 - - + -
61X SER 3.7 2.5 - - - -
62X TYR* 4.1 2.9 - - + -
98X VAL* 3.8 13.7 - - + -
99X PHE* 1.3 77.0 - - - +
101X THR* 1.3 66.1 + - - +
102X CYS* 3.9 4.0 - - - -
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Residues in contact with THR 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X CYS 3.9 1.8 - - - -
21X GLU* 3.9 21.3 + - - +
59X VAL* 3.7 2.1 - - - +
60X ASN* 2.7 50.1 + - - -
61X SER* 3.0 31.6 + - - +
62X TYR* 5.6 0.4 - - - -
63X ARG* 4.7 6.3 - - - +
99X PHE* 3.6 26.0 - - + -
100X VAL* 1.3 74.9 - - - +
102X CYS* 1.3 56.6 + - - +
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Residues in contact with CYS 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 3.7 16.8 - - - -
20X CYS* 2.8 30.2 + - - +
21X GLU* 5.2 2.6 - - - +
51X CYS* 2.1 52.3 - - + -
56X CYS* 3.9 8.3 - - + -
57X GLY 3.7 7.9 - - - +
58X SER 3.5 5.4 - - - -
60X ASN* 3.9 5.6 + - - -
100X VAL* 3.9 1.8 - - - -
101X THR* 1.3 77.0 + - - +
103X GLN* 1.3 71.5 + - - +
104X ASP* 3.8 1.0 + - - +
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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