Contacts of the strand formed by residues 103 - 112 (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 LEU 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D TYR* 4.0 12.6 - - + +
99D GLU* 3.5 2.8 - - - +
100D THR 3.0 29.4 + - - +
101D GLY 3.8 1.2 - - - +
102D LEU* 1.3 80.4 - - + +
104D PHE* 1.3 63.5 + - - +
213D ILE* 3.5 41.3 - - + -
215D LYS* 4.2 21.5 - - - +
228D TYR* 5.1 3.1 - - + +
284D PHE* 3.5 43.3 - - + -
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Residues in contact with PHE 104 (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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30A ASN* 3.9 20.0 - - - -
31A ARG* 3.2 43.5 - - + +
32A ARG* 4.8 6.1 - - - -
98D TYR* 3.2 25.8 + - - +
99D GLU* 4.1 14.8 - - + -
102D LEU 3.4 11.0 - - - -
103D LEU* 1.3 76.9 - - - +
105D GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 105 (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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97D CYS* 3.2 5.9 - - - +
98D TYR* 3.0 49.5 + - - +
104D PHE* 1.3 79.9 - - - +
106D SER* 1.3 59.9 + - - -
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Residues in contact with SER 106 (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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96D GLY 3.3 12.3 - - - -
97D CYS* 3.9 9.0 - - - +
98D TYR* 4.2 1.8 - - - -
105D GLY* 1.3 74.7 - - - -
107D TYR* 1.3 67.0 + - - +
159D GLU* 2.7 43.2 + - - +
163D CYS* 5.2 3.1 - - - -
164D SER* 5.9 3.6 - - - -
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Residues in contact with TYR 107 (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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2D THR* 5.5 1.7 - - - +
3D LEU 3.5 17.0 + - - -
4D LYS* 3.6 15.1 - - - +
94D ILE* 3.8 11.7 - - + -
95D THR* 2.8 29.1 + - - -
96D GLY* 2.8 47.0 + - - +
97D CYS* 3.8 10.2 + - - -
98D TYR* 4.5 4.7 - + + -
106D SER* 1.3 81.9 + - - +
108D GLY* 1.3 59.2 + - - +
109D TYR* 4.1 5.8 - + + -
159D GLU* 3.5 14.5 - - - +
246D GLY 3.5 27.4 - - - -
247D GLU* 4.0 28.5 - - + +
248D PRO* 3.3 24.8 - - + +
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Residues in contact with GLY 108 (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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94D ILE 3.2 8.7 - - - -
95D THR* 3.7 9.4 - - - -
107D TYR* 1.3 78.3 - - - +
109D TYR* 1.3 61.2 + - - +
119D ARG* 3.9 3.4 - - - +
120D TYR* 2.8 33.7 + - - +
155D LEU* 4.1 9.4 - - - -
159D GLU* 3.3 14.6 + - - +
247D GLU* 5.5 0.2 + - - -
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Residues in contact with TYR 109 (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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93D LEU* 3.6 5.8 - - - +
94D ILE* 2.8 61.3 + - + +
107D TYR* 4.1 9.4 - + - -
108D GLY* 1.3 77.5 - - - +
110D VAL* 1.3 69.9 + - - +
111D GLU* 3.3 24.8 + - - -
118D ALA 3.3 13.2 - - - +
119D ARG* 3.8 9.6 - - + +
120D TYR 4.5 0.2 - - - +
127D PHE* 4.9 1.3 - - - -
130D MET* 3.7 23.3 - - + -
243D TYR* 3.7 12.5 - + - -
247D GLU* 3.7 36.1 - - + -
248D PRO* 3.5 10.1 - - + +
249D GLY* 3.2 27.4 + - - -
325D NAG 5.0 1.9 - - - +
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Residues in contact with VAL 110 (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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76D THR* 6.1 0.2 - - + -
91D LEU* 3.6 33.4 - - + -
92D SER 3.2 7.6 - - - +
93D LEU* 3.8 19.5 - - + -
109D TYR* 1.3 76.7 - - - +
111D GLU* 1.3 61.7 + - - +
117D LEU* 2.9 36.2 + - + +
118D ALA 2.7 13.9 + - - +
127D PHE* 3.9 17.9 - - + -
130D MET* 3.1 6.9 - - - +
140D MET* 4.0 19.1 - - + -
141D LEU* 4.2 14.4 - - + -
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Residues in contact with GLU 111 (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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91D LEU* 3.5 7.5 - - - +
92D SER* 2.9 47.2 + - - -
94D ILE* 4.1 12.4 - - + +
109D TYR* 3.3 22.3 + - + -
110D VAL* 1.3 74.8 - - - +
112D THR* 1.3 65.4 + - - +
115D GLY* 3.9 5.6 - - - +
116D PRO* 3.9 16.6 - - + -
117D LEU* 3.9 1.3 - - - +
243D TYR* 3.1 20.1 + - - -
249D GLY* 5.4 1.0 - - - -
325D NAG 4.2 24.7 + - - +
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Residues in contact with THR 112 (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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77D LEU* 6.1 0.2 - - - +
80D ILE* 4.7 5.0 - - - +
86D THR* 5.9 1.5 - - + +
88D THR* 3.2 14.0 + - + +
90D SER* 3.8 7.8 + - - -
91D LEU* 3.7 17.2 - - - +
111D GLU* 1.3 78.6 - - - +
113D ALA* 1.3 64.2 + - - +
114D ASN* 2.8 42.4 - - + +
115D GLY* 2.8 30.5 + - - +
117D LEU* 4.1 17.4 - - - +
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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