Contacts of the strand formed by residues 115 - 121 (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 GLY 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D GLU* 4.2 2.0 - - - -
112D THR* 2.8 32.2 + - - -
113D ALA 3.3 1.2 + - - -
114D ASN* 1.3 82.1 - - - +
116D PRO* 1.3 79.0 - - - +
117D LEU* 3.4 1.7 + - - +
243D TYR* 4.9 0.7 - - - -
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Residues in contact with PRO 116 (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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111D GLU* 3.9 9.4 - - + -
115D GLY* 1.3 85.2 - - - +
117D LEU* 1.3 61.6 + - - +
130D MET* 3.6 27.1 - - + -
131D THR* 3.6 20.2 + - - +
242D ASN* 4.0 27.4 - - + +
243D TYR* 3.1 38.9 - - + +
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Residues in contact with LEU 117 (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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80D ILE* 4.1 16.6 - - + -
86D THR* 5.8 5.4 - - + -
110D VAL* 2.9 29.3 + - + +
111D GLU* 4.4 3.1 - - - -
112D THR* 4.1 21.8 - - - +
115D GLY 3.4 2.6 + - - +
116D PRO* 1.3 76.0 - - - +
118D ALA* 1.3 59.4 + - - +
129D LYS* 3.9 3.5 - - - -
130D MET* 3.1 24.3 + - - +
131D THR* 4.4 1.7 + - - -
134D GLY 4.2 8.0 - - - +
135D PHE* 3.8 29.4 - - + +
136D PRO* 4.2 12.3 - - + -
141D LEU* 4.0 23.3 - - + -
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Residues in contact with ALA 118 (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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109D TYR* 3.3 0.9 - - - -
110D VAL* 2.7 33.1 + - + -
117D LEU* 1.3 83.5 - - + +
119D ARG* 1.3 60.0 + - - +
127D PHE* 3.7 24.9 - - + -
128D THR 3.5 6.3 - - - +
130D MET* 3.2 7.4 - - - +
135D PHE* 3.7 29.8 - - + -
141D LEU* 4.2 8.1 - - + -
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Residues in contact with ARG 119 (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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108D GLY 4.4 4.7 - - - +
109D TYR* 3.8 6.1 - - + -
118D ALA* 1.3 74.0 - - - +
120D TYR* 1.3 67.6 + - - +
121D HIS* 3.5 35.0 + - + +
127D PHE* 3.3 3.2 - - - -
128D THR* 2.7 40.4 + - - +
129D LYS 4.4 4.2 + - - -
130D MET* 3.4 37.8 - - + +
242D ASN 2.9 24.9 + - - -
243D TYR* 3.7 0.8 - - - +
244D GLU* 3.2 28.4 + - - +
247D GLU* 2.8 41.9 + - - +
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Residues in contact with TYR 120 (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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108D GLY 2.8 21.3 + - - +
119D ARG* 1.3 75.3 - - - +
121D HIS* 1.3 74.0 + - - +
122D THR* 4.2 8.1 - - - -
125D LYS* 3.5 25.8 - - - +
126D ARG* 3.7 28.3 - - - -
127D PHE* 3.8 28.6 - + + -
148D TRP* 4.1 12.6 - + - -
151D VAL* 5.2 1.3 - - + -
152D LYS* 3.8 21.6 + - + +
155D LEU* 3.9 13.7 - - + -
156D GLY* 3.3 33.7 - - - -
159D GLU* 3.2 35.8 - - - +
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Residues in contact with HIS 121 (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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119D ARG* 3.5 34.0 + - - -
120D TYR* 1.3 76.0 + - - +
122D THR* 1.3 60.5 + - - +
123D GLY 4.4 2.9 - - - +
124D ASP* 3.7 23.8 - - + +
125D LYS* 2.8 31.5 + - - -
126D ARG 3.0 14.0 + - - +
128D THR* 3.0 37.5 + - + +
244D GLU* 4.7 7.9 - - - -
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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