Contacts of the strand formed by residues 90 - 100 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D THR* 4.3 10.0 - - - +
9D VAL 3.1 16.2 - - - -
10D THR* 3.5 18.6 - - - +
77D LEU* 4.1 7.7 - - - +
88D THR* 3.1 22.1 - - - +
89D THR* 1.3 81.4 - - - +
91D LEU* 1.3 62.3 + - - +
92D SER* 5.1 1.2 + - - -
112D THR* 3.8 3.1 + - - -
113D ALA* 3.4 22.1 + - - +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 3.3 5.5 - - - +
9D VAL* 3.0 39.5 + - + -
73D MET* 3.4 19.8 - - + +
76D THR* 3.5 37.0 - - + -
77D LEU* 4.0 12.5 - - + +
80D ILE* 4.1 13.9 - - + -
90D SER* 1.3 76.1 - - - +
92D SER* 1.3 62.6 + - - +
110D VAL* 3.6 20.6 - - + -
111D GLU 3.5 16.8 - - - +
112D THR* 3.7 16.8 - - - +
117D LEU* 4.5 0.7 - - + -
140D MET* 4.0 12.1 - - + -
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASN* 4.0 6.9 + - - -
7D TYR 3.1 7.6 - - - -
8D THR* 2.9 27.6 + - - +
73D MET* 3.9 4.0 - - - -
90D SER* 5.1 1.9 + - - -
91D LEU* 1.3 74.1 - - - +
93D LEU* 1.3 59.9 + - - +
94D ILE* 3.8 6.2 + - - -
109D TYR 3.8 0.3 - - - +
110D VAL* 3.2 8.8 - - - +
111D GLU* 2.9 54.4 + - - +
325D NAG 4.6 6.2 - - - -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR 3.4 6.4 - - - +
6D ASN* 3.7 0.3 - - - -
7D TYR* 2.8 55.7 + - + -
69D TRP* 3.7 47.8 - - + -
73D MET* 3.8 9.8 - - + +
92D SER* 1.3 71.8 - - - +
94D ILE* 1.3 63.1 + - - +
95D THR* 3.8 3.8 + - + -
109D TYR 3.6 13.9 - - - +
110D VAL* 3.8 18.6 - - + -
140D MET* 4.9 3.8 - - + -
155D LEU* 4.3 28.9 - - + -
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LYS* 4.6 4.5 - - + -
5D TYR 3.6 4.0 - - - +
6D ASN* 3.4 36.3 - - + +
92D SER* 4.2 6.7 - - - -
93D LEU* 1.3 73.0 - - - +
95D THR* 1.3 63.4 + - - +
107D TYR* 3.8 7.5 - - + -
108D GLY* 3.2 1.7 - - - -
109D TYR* 2.8 70.2 + - + +
111D GLU* 4.1 16.2 - - + +
248D PRO* 3.4 33.0 - - + -
325D NAG 4.0 17.5 - - + +
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Residues in contact with THR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 2.7 55.6 + - + +
7D TYR* 4.7 11.0 - - + -
93D LEU* 5.0 4.7 - - + +
94D ILE* 1.3 77.8 - - - +
96D GLY* 1.3 54.3 + - - +
107D TYR* 2.8 26.3 + - - -
108D GLY* 3.9 0.2 - - - -
155D LEU* 3.6 27.6 - - + +
158D PHE* 3.7 24.1 - - + -
159D GLU* 4.7 3.8 - - - +
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Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU 3.1 13.2 - - - -
4D LYS* 4.4 0.2 - - - -
5D TYR 4.6 0.2 - - - -
95D THR* 1.3 77.7 + - - +
97D CYS* 1.3 61.5 + - - +
106D SER* 3.3 4.2 - - - -
107D TYR* 2.8 44.0 + - - +
158D PHE* 4.3 3.1 - - - -
159D GLU* 5.8 0.3 - - - -
163D CYS* 3.6 15.2 - - - +
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Residues in contact with CYS 97 (chain D).
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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2D THR* 3.8 2.4 + - - +
3D LEU* 2.9 29.6 + - - +
96D GLY* 1.3 75.7 - - - +
98D TYR* 1.3 68.4 + - - +
105D GLY 3.2 15.3 - - - +
106D SER* 3.9 9.6 - - - +
107D TYR* 3.8 6.1 + - - -
163D CYS* 3.2 42.2 - - + -
164D SER* 3.8 10.8 - - - +
167D ILE* 3.8 25.1 - - - -
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Residues in contact with TYR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ILE 3.5 11.7 - - - +
2D THR* 3.9 9.6 - - - +
97D CYS* 1.3 85.1 - - - +
99D GLU* 1.3 63.2 + - - +
100D THR* 3.6 22.7 - - - +
103D LEU* 4.0 5.4 - - + +
104D PHE* 3.2 23.5 + - - +
105D GLY* 3.0 53.6 + - - +
106D SER 4.2 2.0 - - - -
107D TYR* 4.5 5.8 - + + -
167D ILE* 4.5 3.1 - - - -
211D ASP* 5.7 0.2 - - + -
213D ILE* 4.3 15.9 - - + +
245D PRO 4.0 9.9 + - - -
246D GLY* 3.6 36.1 - - - +
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.2 38.4 + - - +
32A ARG* 2.7 43.6 + - - -
1D ILE* 2.9 52.6 + - + +
98D TYR* 1.3 75.0 - - - +
100D THR* 1.3 60.2 + - - +
101D GLY 3.5 3.7 + - - +
103D LEU 3.5 4.9 - - - -
104D PHE* 4.1 9.0 - - + -
164D SER 5.4 0.5 - - - +
167D ILE* 4.9 7.8 - - + +
168D LEU* 4.0 7.7 - - - +
286D ASP* 3.0 7.6 - - - +
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Residues in contact with THR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TYR* 3.6 22.5 - - - +
99D GLU* 1.3 68.2 - - - +
101D GLY* 1.3 66.2 + - - +
102D LEU 3.2 0.5 + - - -
103D LEU* 3.0 24.3 + - - +
211D ASP* 3.1 42.2 + - - +
212D VAL 4.1 0.4 - - - +
213D ILE* 3.9 27.0 - - + +
284D PHE* 3.2 29.8 - - - +
285D HIS* 4.3 1.6 - - - -
286D ASP* 4.0 1.1 - - - +
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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