Contacts of the strand formed by residues 123 - 130 (chain A) in PDB entry 5INQ
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 THR 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS* 3.3 24.4 + - - -
119A GLU 5.0 1.3 - - - +
120A ASP* 3.1 34.1 + - + +
121A SER 4.3 1.6 - - - +
122A SER* 1.3 85.9 - - - +
124A ILE* 1.3 63.9 + - - +
125A SER* 4.7 4.5 + - - -
156A ASP* 3.6 0.9 + - - +
225A LEU* 5.3 1.0 - - - +
365A THR* 5.4 6.8 - - - +
366A LEU 3.2 9.2 - - - -
367A ASN* 3.1 23.3 - - - +
368A VAL* 5.4 0.7 - - - -
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER 4.2 0.8 + - - -
123A THR* 1.3 74.4 - - - +
125A SER* 1.3 71.2 + - - +
126A PHE* 4.6 8.8 - - + -
156A ASP* 3.4 4.9 - - + +
157A VAL* 4.3 14.8 - - + -
159A PHE* 6.4 0.2 - - + -
225A LEU* 3.6 29.6 - - + -
230A PHE* 4.1 37.7 - - + -
232A LEU* 4.4 8.1 - - + -
268A ILE* 4.4 10.1 - - + -
337A LEU* 5.0 0.4 - - + -
364A CYS 4.0 0.7 - - - +
365A THR* 3.4 1.9 - - - -
366A LEU* 2.9 62.2 + - + +
368A VAL* 4.8 4.8 - - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LYS* 6.1 0.2 - - - +
123A THR* 4.1 4.7 + - - -
124A ILE* 1.3 76.5 - - - +
126A PHE* 1.3 63.3 + - - +
153A TYR 5.0 1.9 + - - -
154A SER 4.3 2.6 + - - -
155A PRO* 3.4 10.4 - - - +
156A ASP* 2.9 41.3 + - - +
157A VAL 3.3 3.8 + - - -
198A ARG* 5.1 0.2 + - - -
363A LEU* 5.1 5.6 - - - -
364A CYS 3.3 4.9 - - - -
365A THR* 3.8 21.8 - - - -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 4.6 15.3 - - + -
125A SER* 1.3 78.6 - - - +
127A ILE* 1.3 68.7 + - - +
128A THR* 4.8 2.0 - - + -
155A PRO* 3.8 3.4 - - - -
157A VAL* 3.1 22.4 - - + +
159A PHE* 3.5 28.5 - + + -
268A ILE* 4.1 13.9 - - + -
270A ALA* 3.8 14.8 - - + -
328A ILE* 3.7 40.6 - - + -
362A LEU 5.0 0.7 - - - -
363A LEU* 3.4 5.0 - - - +
364A CYS* 2.8 55.0 + - + +
366A LEU* 4.0 24.7 - - + -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 1.3 80.9 - - - +
128A THR* 1.3 72.7 + - - +
129A TRP* 4.2 22.9 - - + -
149A CYS* 4.0 23.1 - - - +
150A LEU* 4.0 20.6 - - + -
153A TYR* 4.5 8.3 - - + -
155A PRO* 4.1 14.3 - - + +
157A VAL 3.2 4.8 + - - -
158A VAL* 3.3 16.1 - - + +
159A PHE* 2.8 27.9 + - - +
345A VAL* 4.4 8.5 - - + -
362A LEU 3.1 11.2 - - - +
363A LEU* 3.7 24.2 - - + -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.4 1.3 - - + -
127A ILE* 1.3 72.4 - - - +
129A TRP* 1.3 65.3 + - - +
159A PHE* 3.2 6.6 + - - -
161A GLN* 3.3 20.4 + - - -
270A ALA* 3.5 25.3 + - + -
271A GLY* 3.5 16.6 + - - +
326A ASP* 5.0 10.0 + - + +
327A ARG 5.0 1.3 - - - +
328A ILE* 4.3 9.0 - - + -
360A TRP 4.8 0.3 - - - +
361A GLY* 3.4 1.2 - - - -
362A LEU* 3.0 60.2 + - + +
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Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 4.2 17.5 - - + -
128A THR* 1.3 78.0 + - - +
130A ASN* 1.3 81.4 + - - +
131A ILE* 3.5 14.0 + - + -
145A GLY 5.0 0.2 - - - -
146A VAL* 3.9 36.8 - - + -
149A CYS* 4.0 28.3 - - + -
150A LEU* 5.4 2.5 - - + -
159A PHE 2.9 8.7 + - - -
160A LEU* 3.3 16.2 - - + +
161A GLN* 3.0 23.2 + - - -
326A ASP* 5.2 1.6 - - - -
345A VAL* 4.2 3.8 - - + -
346A GLY* 3.6 34.8 - - - -
356A PRO* 3.8 21.5 - - + -
357A SER* 3.8 6.6 - - - -
359A HIS* 3.1 21.6 + - + -
360A TRP 3.9 5.2 - - - -
361A GLY* 3.4 20.7 - - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 1.3 77.7 - - - +
131A ILE* 1.3 53.7 + - - +
132A ASP* 3.0 17.3 + - - +
161A GLN* 3.1 24.6 + - - +
162A GLU* 3.1 32.5 + - - +
236A HIS* 3.6 9.9 + - - -
272A ASP* 2.9 27.6 + - - +
326A ASP* 4.3 5.7 + - - +
357A SER* 2.6 25.1 + - - -
358A ASP* 4.6 0.2 - - - +
359A HIS* 3.6 28.6 + - + +
1D C 4.3 0.2 - - - -
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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