Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 5T1I
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 PRO 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B PHE* 4.6 5.4 - - + -
121B LEU 3.5 8.9 - - - +
122B ASP* 1.3 90.2 - - - +
124B GLU* 1.3 62.6 + - - +
140B MET* 3.7 25.8 - - + -
141B LYS 4.1 0.9 - - - +
142B TRP* 3.6 19.3 - - + -
143B LYS* 3.6 5.9 - - - -
159B LYS 5.5 1.1 - - - +
160B CYS* 3.7 29.4 - - + -
163B ILE* 4.1 7.2 - - + +
206B UNX 2.7 30.4 - - - -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASP 3.4 1.0 + - - -
123B PRO* 1.3 75.1 - - - +
125B ARG* 1.3 83.8 + - - +
141B LYS* 2.8 39.8 + - + +
142B TRP 4.0 0.2 - - - -
143B LYS* 3.5 42.5 - - + +
144B ASP 4.2 1.7 + - - -
163B ILE* 3.6 17.5 - - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 1.3 108.0 + - - +
126B ILE* 1.3 75.1 + - - +
127B ILE* 3.9 21.4 - - + +
140B MET* 3.9 6.2 - - - -
141B LYS* 2.8 41.9 + - + +
163B ILE* 4.1 6.3 - - - -
166B ALA* 6.3 3.1 - - + -
167B PHE* 6.2 2.7 - - - +
171B ARG* 6.2 1.6 - - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG* 1.3 86.2 - - - +
127B ILE* 1.3 62.4 + - - +
128B GLY 3.3 22.0 - - - +
138B PHE* 3.7 43.1 - - + -
139B LEU 3.5 5.6 - - - +
140B MET* 3.7 23.1 - - + -
163B ILE* 3.9 12.8 + - + +
164B VAL* 3.8 31.2 - - + -
167B PHE* 3.4 40.2 - - + +
171B ARG* 4.4 4.3 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG* 3.8 39.0 - - - +
126B ILE* 1.3 80.1 - - - +
128B GLY* 1.3 58.9 + - - +
139B LEU* 2.9 34.1 + - + +
141B LYS* 4.0 15.5 - - + +
148B ALA* 4.0 23.6 - - + -
167B PHE* 4.4 4.9 - - - -
171B ARG* 4.5 10.9 + - - +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.3 13.4 - - - +
127B ILE* 1.3 79.8 - - - +
129B ALA* 1.3 62.8 + - - +
138B PHE* 3.5 0.9 - - - -
139B LEU* 2.9 33.7 + - - -
167B PHE* 4.1 8.4 - - - -
207B UNX 3.2 13.2 - - - -
51C ILE* 4.3 4.3 - - - -
101C UNX 4.5 1.1 - - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TRP* 3.9 20.3 - - + -
128B GLY* 1.3 74.8 - - - +
130B THR* 1.3 62.0 + - - +
136B LEU* 4.6 2.7 - - + -
137B MET 3.3 12.1 - - - +
138B PHE* 4.3 5.8 - - + +
139B LEU 4.6 0.2 - - - +
167B PHE* 4.3 13.0 - - + -
207B UNX 3.0 6.3 - - - -
48C LEU* 4.2 17.3 - - + -
49C ARG 3.5 6.6 - - - +
51C ILE* 3.3 28.3 + - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TRP* 4.0 5.4 - - - -
129B ALA* 1.3 75.8 - - - +
131B ASP* 1.3 59.7 + - - +
132B SER* 3.2 11.6 + - - +
135B GLU 3.9 0.7 - - - +
136B LEU* 3.7 3.6 - - - +
137B MET* 2.9 56.2 + - + +
150B LEU* 3.9 24.9 - - + -
50C GLU* 2.5 27.1 + - - -
51C ILE* 4.5 9.6 - - + -
52C AAR 3.6 14.4 + - + +
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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