Contacts of the strand formed by residues 92 - 99 (chain L) in PDB entry 2A3W
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 92 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L ARG* 3.3 7.2 - - - +
39L ALA* 2.9 48.2 + - + +
65L LYS* 6.2 0.7 - - - +
71L TYR* 3.8 17.5 - - + +
86L GLU* 4.6 4.5 - - - +
90L ALA 4.3 6.1 - - - +
91L PRO* 1.3 76.0 - - - +
93L HIS* 1.3 68.5 + - - +
94L ILE* 3.8 23.9 + - + -
109L ILE* 3.7 29.8 - - + -
110L ASN* 3.6 10.3 - - - +
203L TRP* 4.8 0.6 - - - -
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Residues in contact with HIS 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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36L CYS* 4.1 6.7 - - - +
37L PHE* 3.6 18.2 + - - -
38L ARG* 3.7 32.5 - - + +
92L VAL* 1.3 75.5 - - - +
94L ILE* 1.3 61.1 + - - +
95L CYS* 3.4 32.7 + - - -
108L TRP* 3.5 1.9 + - - +
109L ILE* 3.5 4.3 - - - -
110L ASN* 2.8 36.4 + - - -
111L GLY 5.0 3.2 + - - -
156L ASP* 5.1 4.6 + - + +
169L ILE* 5.6 1.0 - - + +
172L ALA* 3.6 15.8 + - + +
173L TYR* 3.4 53.9 - + + +
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Residues in contact with ILE 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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35L LEU 3.8 0.3 - - - +
36L CYS* 3.2 2.8 - - - -
37L PHE* 2.8 78.5 + - + +
39L ALA* 4.8 2.0 - - + -
49L LEU* 3.9 11.9 - - + -
63L VAL* 5.0 2.5 - - + -
71L TYR* 3.7 22.0 - - + -
92L VAL* 3.8 23.6 - - + +
93L HIS* 1.3 77.0 - - - +
95L CYS* 1.3 76.6 + - - +
96L VAL* 4.8 1.1 - - + +
107L PHE* 4.2 16.4 - - + -
108L TRP 3.4 2.9 - - - -
109L ILE* 3.8 24.0 - - + -
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Residues in contact with CYS 95 (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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34L THR* 4.9 0.2 - - + -
35L LEU 3.2 4.0 - - - -
36L CYS* 2.0 46.9 - - - -
93L HIS* 3.4 19.5 - - - -
94L ILE* 1.3 73.3 - - - +
96L VAL* 1.3 61.7 + - - +
106L GLU 4.3 0.2 - - - -
107L PHE* 3.4 6.8 - - - -
108L TRP* 2.7 49.2 + - + +
169L ILE* 3.8 30.1 - - + -
172L ALA* 4.5 1.8 - - - -
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Residues in contact with VAL 96 (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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33L PHE* 3.8 6.4 - - + -
34L THR* 3.4 2.8 - - - -
35L LEU* 2.8 52.5 + - + +
37L PHE* 5.7 0.4 - - + -
63L VAL* 3.8 28.5 - - + -
73L LEU* 4.1 26.9 - - + -
94L ILE* 5.3 2.0 - - + -
95L CYS* 1.3 75.6 - - - +
97L SER* 1.3 65.5 + - - +
105L ALA* 5.1 0.2 - - + -
106L GLU 3.1 14.8 - - - +
107L PHE* 3.8 33.7 - - + -
108L TRP* 5.8 0.2 - - - -
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Residues in contact with SER 97 (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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33L PHE* 3.2 7.4 - - - -
34L THR* 3.5 24.2 - - - -
96L VAL* 1.3 76.6 - - - +
98L TRP* 1.3 62.1 + - - +
104L ILE 5.1 0.9 + - - -
105L ALA* 3.3 5.7 - - - +
106L GLU* 2.9 57.7 + - - +
108L TRP* 5.5 2.4 - - - -
163L VAL* 3.6 18.7 - - - +
164L LEU 4.9 2.2 - - - -
169L ILE* 5.8 2.0 - - - -
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Residues in contact with TRP 98 (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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30L LEU 4.1 1.3 - - - -
31L GLN 3.7 17.5 - - - -
32L ASN* 3.4 4.7 - - - -
33L PHE* 2.9 57.3 + + + +
73L LEU* 4.2 6.3 - - + -
75L ILE* 3.9 26.9 - - + -
97L SER* 1.3 75.4 - - - +
99L GLU* 1.3 66.5 - - - +
100L SER* 3.7 11.0 - - - -
103L GLY* 3.2 19.6 + - - -
104L ILE 3.4 10.5 - - - -
105L ALA* 4.2 2.0 - - + -
119L LEU* 3.0 35.5 + - + +
120L ARG 3.3 22.2 - - - -
123L TYR* 3.2 28.3 - + - -
125L VAL* 3.5 29.8 - - + -
163L VAL* 3.6 5.1 - - - +
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Residues in contact with GLU 99 (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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199K LYS* 2.9 25.8 + - - -
32L ASN* 3.4 18.9 + - - +
98L TRP* 1.3 80.3 - - - +
100L SER* 1.3 55.1 + - - +
101L SER* 3.4 19.3 + - - +
102L SER* 2.6 27.1 + - - +
103L GLY* 2.7 36.0 + - - -
104L ILE* 3.2 10.2 + - + +
163L VAL* 3.8 21.9 - - + +
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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