Contacts of the strand formed by residues 90 - 100 (chain L) in PDB entry 3IT8
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 SER 90 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8L THR* 4.3 10.2 - - - +
9L VAL 3.1 15.7 - - - -
10L THR* 3.5 19.0 - - - +
77L LEU* 4.1 6.9 - - - +
88L THR* 3.1 21.5 - - - +
89L THR* 1.3 83.2 - - - +
91L LEU* 1.3 63.7 - - - +
92L SER* 5.1 1.4 + - - -
112L THR* 3.8 3.3 + - - -
113L ALA* 3.5 21.7 + - - +
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Residues in contact with LEU 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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8L THR* 3.3 4.9 - - - +
9L VAL* 3.0 40.5 + - + -
73L MET* 3.4 18.4 - - + +
76L THR* 3.6 36.8 - - + -
77L LEU* 4.1 11.9 - - + +
80L ILE* 4.1 14.4 - - + -
90L SER* 1.3 76.7 - - - +
92L SER* 1.3 63.6 + - - +
110L VAL* 3.5 19.7 - - + -
111L GLU 3.5 16.2 - - - +
112L THR* 3.7 16.2 - - - +
117L LEU* 4.5 0.9 - - + -
140L MET* 4.0 13.2 - - + -
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Residues in contact with SER 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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6L ASN* 4.1 7.3 + - - -
7L TYR 3.1 7.6 - - - -
8L THR* 2.9 27.7 + - - +
73L MET* 3.9 4.3 - - - -
90L SER* 5.1 1.7 + - - -
91L LEU* 1.3 73.4 - - - +
93L LEU* 1.3 60.4 + - - +
94L ILE* 3.8 5.7 + - - -
109L TYR 3.8 0.2 - - - +
110L VAL* 3.2 9.5 - - - +
111L GLU* 2.9 53.7 + - - +
325L NAG 4.5 7.7 - - - -
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Residues in contact with LEU 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 TYR 3.4 6.2 - - - +
6L ASN* 3.7 0.3 - - - -
7L TYR* 2.8 54.3 + - + -
69L TRP* 3.7 48.0 - - + -
73L MET* 3.7 10.4 - - + +
92L SER* 1.3 71.0 - - - +
94L ILE* 1.3 64.4 + - - +
95L THR* 3.8 3.5 + - + -
109L TYR 3.6 14.4 - - - +
110L VAL* 3.8 17.5 - - + +
140L MET* 5.0 4.3 - - + -
155L LEU* 4.3 29.6 - - + -
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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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4L LYS* 4.7 4.3 - - + -
5L TYR 3.6 3.4 - - - +
6L ASN* 3.3 33.0 - - + +
92L SER* 4.2 5.2 - - - -
93L LEU* 1.3 72.6 - - - +
95L THR* 1.3 62.0 + - - +
107L TYR* 3.8 5.3 - - + -
108L GLY* 3.2 3.1 + - - -
109L TYR* 2.7 72.5 + - + +
111L GLU* 4.0 11.4 - - + -
248L PRO* 3.4 33.0 - - + -
325L NAG 3.5 28.0 - - + +
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Residues in contact with THR 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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4L LYS 3.7 0.2 - - - -
5L TYR* 2.7 57.3 + - + +
7L TYR* 4.7 10.5 - - + -
93L LEU* 5.0 6.1 - - + +
94L ILE* 1.3 76.0 - - - +
96L GLY* 1.3 54.0 + - - +
107L TYR* 2.8 26.0 + - - -
108L GLY* 3.8 4.2 - - - -
155L LEU* 3.7 22.9 - - + +
158L PHE* 3.8 22.9 - - + -
159L GLU* 4.7 4.7 - - - +
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Residues in contact with GLY 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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3L LEU 3.1 13.9 - - - -
5L TYR 4.6 0.2 - - - -
95L THR* 1.3 77.8 + - - +
97L CYS* 1.3 61.8 + - - +
106L SER* 3.3 4.0 - - - -
107L TYR* 2.8 43.5 + - - +
158L PHE* 4.3 2.9 - - - -
159L GLU* 5.8 0.2 - - - -
163L CYS* 3.6 15.2 - - - +
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Residues in contact with CYS 97 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2L THR* 3.9 1.9 + - - -
3L LEU* 2.9 30.4 + - - +
96L GLY* 1.3 75.7 - - - +
98L TYR* 1.3 68.8 + - - +
105L GLY 3.2 16.2 - - - +
106L SER* 3.9 10.3 - - - +
107L TYR* 3.8 6.7 + - - -
163L CYS* 3.2 40.6 - - + -
164L SER* 3.9 10.1 - - - +
167L ILE* 3.8 25.6 - - - -
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Residues in contact with TYR 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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1L ILE 3.5 11.4 - - - +
2L THR* 3.9 9.6 - - - +
97L CYS* 1.3 86.2 - - - +
99L GLU* 1.3 62.7 + - - +
100L THR* 3.6 21.8 - - - +
103L LEU* 4.0 5.0 - - + +
104L PHE* 3.2 33.3 + - - +
105L GLY* 3.0 42.1 + - - +
106L SER 4.1 2.0 - - - -
107L TYR* 4.5 6.1 - + + -
167L ILE* 4.5 3.8 - - - -
211L ASP* 5.7 0.2 - - + -
213L ILE* 4.3 16.3 - - + +
245L PRO 4.0 10.4 + - - -
246L GLY* 3.6 36.1 - - - +
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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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31I ARG* 3.2 37.4 + - - +
32I ARG* 2.7 45.1 + - - -
1L ILE* 2.9 53.3 + - + +
98L TYR* 1.3 75.8 - - - +
100L THR* 1.3 60.1 + - - +
101L GLY 3.5 3.2 + - - +
103L LEU 3.5 5.2 - - - -
104L PHE* 4.1 8.1 - - + -
164L SER 5.4 0.7 - - - +
167L ILE* 5.0 7.2 - - + +
168L LEU* 4.0 8.1 - - - +
286L ASP* 3.0 7.4 - - - +
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Residues in contact with THR 100 (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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98L TYR* 3.6 22.5 - - - +
99L GLU* 1.3 68.8 - - - +
101L GLY* 1.3 65.0 + - - +
102L LEU 3.2 0.3 + - - -
103L LEU* 3.0 24.3 + - - +
211L ASP* 3.0 41.7 + - - +
212L VAL* 3.9 1.3 - - - -
213L ILE* 3.9 27.8 - - + +
284L PHE* 3.3 29.5 - - - +
285L HIS* 4.3 1.6 - - - -
286L ASP* 4.0 0.9 - - - -
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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