Contacts of the strand formed by residues 117 - 127 (chain A) in PDB entry 4TZJ
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 ILE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.7 30.7 - - + -
108A PHE 3.5 6.5 - - - +
109A TYR* 4.7 3.4 - - + -
114A GLU 3.9 20.9 - - - +
115A GLU* 3.2 7.6 + - - +
116A ASP* 1.3 75.4 + - - +
118A ASN* 1.3 66.0 + - - +
119A GLU 3.5 24.0 - - - +
120A VAL* 4.5 0.2 - - + -
191A ARG* 4.0 9.2 - - - +
214A TYR* 4.2 11.2 - - + -
215A THR 3.5 25.4 + - - +
216A LEU* 3.7 24.1 - - + +
217A ASN* 4.4 8.8 + - - +
220A ILE* 5.3 2.1 - - - +
242A GLN* 4.2 10.7 + - - -
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Residues in contact with ASN 118 (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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108A PHE* 2.7 11.5 + - + +
109A TYR* 3.6 6.1 - - - +
110A LYS* 3.5 46.7 - - - +
116A ASP* 4.0 13.8 + - - +
117A ILE* 1.3 80.4 - - - +
119A GLU* 1.3 61.9 + - + +
186A SER* 5.0 1.4 + - - -
220A ILE* 4.1 4.5 - - - +
241A SER* 3.6 1.6 + - - -
242A GLN* 3.0 45.1 + - + +
243A TYR* 3.4 29.8 + - + +
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Residues in contact with GLU 119 (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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54A ARG* 3.0 42.0 + - - -
107A VAL* 3.4 2.4 - - - -
108A PHE* 2.7 64.7 + - + -
117A ILE* 3.5 5.2 - - - +
118A ASN* 1.3 82.8 - - - +
120A VAL* 1.3 65.4 + - - +
121A PHE* 3.3 18.0 - - + -
179A MET* 3.5 9.5 - - - +
220A ILE* 5.4 0.4 - - - -
240A ALA 3.3 13.2 - - - +
241A SER* 2.5 27.2 + - - +
243A TYR* 3.2 5.3 - - + -
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Residues in contact with VAL 120 (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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105A ALA* 4.1 4.0 - - + -
106A ILE 3.2 11.7 - - - +
107A VAL* 3.7 21.1 - - + -
117A ILE* 4.5 2.5 - - + -
119A GLU* 1.3 76.9 - - - +
121A PHE* 1.3 75.0 + - - +
122A ALA* 4.0 1.8 - - + +
141A ILE* 4.2 6.5 - - + -
214A TYR* 3.9 22.0 - - + +
216A LEU* 3.8 25.1 - - + -
239A ALA* 3.2 7.1 - - - +
240A ALA* 2.9 58.2 + - + +
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Residues in contact with PHE 121 (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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50A ILE* 3.5 48.7 - - + -
54A ARG* 4.8 1.8 - - + -
105A ALA* 3.3 1.2 - - - -
106A ILE* 2.8 45.7 + - + +
108A PHE* 4.2 6.3 - + - -
119A GLU* 3.3 31.9 - - + -
120A VAL* 1.3 74.6 - - - +
122A ALA* 1.3 62.2 + - - +
123A PHE* 4.0 10.3 - - + -
172A LEU* 4.1 23.1 - - + -
175A CYS* 5.4 2.5 - - - -
176A ILE* 4.1 20.9 - - + -
179A MET* 3.8 22.7 - - + -
237A MET* 5.1 4.5 - - + -
238A LEU 3.7 2.9 - - - -
239A ALA* 4.0 18.8 - - + -
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Residues in contact with ALA 122 (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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103A GLU* 3.4 25.4 - - - +
104A PHE 3.9 2.9 - - - -
105A ALA* 4.0 4.0 - - + -
120A VAL* 4.0 2.9 - - + -
121A PHE* 1.3 73.9 - - - +
123A PHE* 1.3 62.1 + - - +
124A ARG* 4.1 2.0 - - + -
141A ILE* 3.7 22.0 - - + -
214A TYR* 3.7 5.4 - - - +
236A GLN 3.6 0.7 - - - +
237A MET* 3.3 8.0 - - - +
238A LEU* 2.7 41.7 + - + +
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Residues in contact with PHE 123 (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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42A TYR* 4.5 5.2 - + - -
43A ILE* 3.8 35.0 - - + -
46A ALA* 3.6 26.7 - - + -
47A SER* 4.5 2.9 - - - -
50A ILE* 4.1 19.1 - - + -
103A GLU* 3.2 3.4 - - - +
104A PHE* 2.8 68.9 + + + +
106A ILE* 4.6 2.0 - - + -
121A PHE* 4.0 15.5 - - + -
122A ALA* 1.3 75.1 - - - +
124A ARG* 1.3 61.9 + - - +
125A PHE* 3.7 10.5 - - + -
235A ILE* 4.4 10.1 - - + -
236A GLN 3.4 4.3 - - - +
237A MET* 3.6 38.1 - - + -
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Residues in contact with ARG 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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102A ARG* 3.5 21.9 - - - +
103A GLU* 2.3 57.7 + - - +
122A ALA* 5.1 2.7 - - + -
123A PHE* 1.3 75.0 - - - +
125A PHE* 1.3 62.4 + - - +
133A ILE* 3.7 26.3 - - - +
134A PHE 5.1 1.4 + - - -
141A ILE* 5.0 0.7 - - - -
142A ASP* 3.5 45.1 + - - +
147A SER* 6.0 1.2 - - - -
150A LEU* 4.4 10.8 - - + +
193A SER* 4.5 2.8 + - - -
234A LYS 3.5 3.3 - - - +
235A ILE* 3.5 2.1 - - - -
236A GLN* 2.9 58.4 + - - +
238A LEU* 4.3 12.8 - - + -
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Residues in contact with PHE 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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39A ALA* 4.2 11.7 - - + -
43A ILE* 3.9 23.6 - - + -
96A ILE* 3.8 32.1 - - + -
101A LEU* 3.6 30.5 - - + +
102A ARG* 2.7 50.5 + - - +
104A PHE* 4.5 4.5 - - + -
123A PHE* 3.7 24.0 - - + -
124A ARG* 1.3 79.2 - - - +
126A ALA* 1.3 62.6 + - - +
127A TYR* 4.0 19.5 - + + -
133A ILE* 4.0 5.5 - - - +
150A LEU* 4.1 2.8 - - - +
233A HIS* 5.2 5.4 - - + -
234A LYS 3.5 4.0 - - - -
235A ILE* 4.0 21.8 - - + -
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Residues in contact with ALA 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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125A PHE* 1.3 77.2 - - - +
127A TYR* 1.3 62.9 + - - +
130A GLU* 3.3 13.9 - - + +
133A ILE* 4.6 6.5 - - + -
150A LEU* 4.0 15.0 - - + -
232A HIS 3.6 0.3 - - - +
233A HIS* 3.3 4.8 - - - -
234A LYS* 2.8 67.1 + - - +
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Residues in contact with TYR 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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96A ILE* 3.4 31.9 - - + +
99A GLY* 3.6 27.1 - - - -
101A LEU* 2.5 47.8 + - - +
102A ARG* 4.7 0.9 - - - -
125A PHE* 4.0 17.0 - + + -
126A ALA* 1.3 70.2 - - - +
128A GLY* 1.3 68.0 + - - +
129A ASP 3.3 2.2 - - - -
130A GLU* 2.3 58.8 + - + +
195A THR* 4.3 8.3 - - + -
232A HIS 3.2 4.9 - - - +
233A HIS* 3.4 28.7 - + - -
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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