Contacts of the strand formed by residues 88 - 94 (chain L) in PDB entry 2CHT
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 CYS 88 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9L ALA* 4.6 3.8 - - - -
10L THR 3.3 9.9 - - - -
11L THR* 3.8 6.5 - - + -
48L SER 4.4 0.2 - - - -
49L ALA* 3.2 4.0 - - - -
50L THR* 3.1 28.8 + - - +
53L LEU* 3.9 1.0 - - - +
85L LEU* 3.8 31.0 - - + +
86L LYS 3.6 9.9 - - - +
87L LYS* 1.3 74.7 - - - +
89L ILE* 1.3 63.9 + - - +
90L ARG* 3.2 43.9 + - - +
112L ALA* 4.7 0.7 - - - -
115L LEU* 4.3 4.9 - - - -
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Residues in contact with ILE 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA* 3.3 3.1 - - - +
10L THR* 2.8 52.4 + - + +
12L VAL* 3.5 31.6 - - + -
20L ILE* 4.9 6.7 - - + +
23L LYS* 5.1 0.2 - - + -
24L THR* 4.1 20.6 - - + +
27L LEU* 4.5 7.5 - - + +
47L LEU* 4.9 3.8 - - + -
48L SER 3.2 15.7 - - - +
49L ALA* 4.5 1.1 - - + -
53L LEU* 4.1 16.2 - - + -
58L PRO* 3.8 31.9 - - + -
87L LYS 4.2 1.8 - - - +
88L CYS* 1.3 75.8 - - - +
90L ARG* 1.3 65.3 + - - +
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Residues in contact with ARG 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K PHE* 3.6 15.6 - - - -
74K THR* 4.1 4.7 - - - +
7L ARG* 3.4 18.4 - - - +
8L GLY 3.5 5.4 - - - -
9L ALA* 3.8 12.3 - - + +
47L LEU* 3.5 3.8 - - - -
48L SER* 2.9 38.8 + - - +
50L THR* 3.8 12.1 - - - +
78L GLU* 3.2 42.4 - - - +
85L LEU* 5.0 7.1 + - - +
88L CYS* 3.2 26.8 + - - +
89L ILE* 1.3 77.7 - - - +
91L VAL* 1.3 62.7 + - - +
115L LEU* 3.9 16.3 - - - +
211L TSA 2.9 48.0 + - - +
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Residues in contact with VAL 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K THR* 5.7 1.3 - - - -
7L ARG* 3.0 22.6 + - - -
8L GLY* 3.1 42.9 + - - +
27L LEU* 3.6 17.7 - - + -
28L LEU* 4.0 13.5 - - + -
31L ILE* 3.7 15.7 - - + -
45L MET* 4.1 12.6 - - + -
46L LEU 3.5 6.7 - - - +
47L LEU* 3.6 25.1 - - + -
90L ARG* 1.3 75.3 - - - +
92L MET* 1.3 65.7 + - - +
93L MET* 4.0 4.3 - - + +
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Residues in contact with MET 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K GLN* 3.5 38.4 - - - +
45K MET 4.9 2.9 - - - +
46K LEU* 5.1 2.0 - - + -
72K PRO* 3.7 15.9 - - + +
73K VAL 4.9 0.9 - - - -
74K THR* 4.3 20.0 - - + -
5L GLY* 3.5 14.1 - - - -
6L ILE 3.4 45.1 - - - +
7L ARG* 3.7 17.9 - - - -
45L MET* 3.5 2.8 - - - -
46L LEU* 3.1 53.2 + - + +
91L VAL* 1.3 74.7 - - - +
93L MET* 1.3 56.2 + - - +
94L THR* 4.0 2.0 + - - +
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Residues in contact with MET 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L GLY* 3.4 1.8 - - - -
6L ILE* 2.7 49.7 + - + +
28L LEU* 5.8 3.6 - - - -
31L ILE* 3.6 35.2 - - + -
32L ILE* 4.6 6.1 - - + -
37L THR* 3.6 35.2 - - + +
42L VAL* 4.0 11.0 - - + -
44L GLN 4.0 3.6 - - - -
45L MET* 4.2 17.0 - - + +
68L TRP* 4.0 27.1 - - + -
91L VAL* 4.0 7.1 - - + -
92L MET* 1.3 70.7 - - - +
94L THR* 1.3 59.9 + - - +
95L VAL* 3.6 16.5 + - + -
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Residues in contact with THR 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K VAL* 3.6 17.9 - - + -
44K GLN* 2.6 36.0 + - - +
94K THR* 5.9 0.4 - - + -
3L ILE* 3.6 19.3 - - + -
4L ARG 3.3 13.0 - - - +
42L VAL* 3.6 3.1 - - - +
43L VAL* 2.9 34.6 + - + +
44L GLN* 3.1 25.5 + - - +
92L MET 4.5 3.1 + - - -
93L MET* 1.3 70.1 - - - +
95L VAL* 1.3 58.8 + - - +
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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