Contacts of the strand formed by residues 105 - 119 (chain D) in PDB entry 3ZJX
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 PHE 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D VAL* 4.0 18.8 - - + -
103D GLN* 3.6 14.8 - - + -
104D SER* 1.3 76.0 + - - +
106D THR* 1.3 76.0 + - - +
107D CYS* 5.0 1.3 - - - -
163D ASN* 3.7 0.3 - - - -
164D VAL* 2.8 75.0 + - + +
165D PRO 4.9 2.5 - - - -
181D ALA* 4.1 18.2 - - + -
252D LEU* 4.6 9.4 - - + -
254D VAL* 5.4 1.6 - - + -
1296D BOG 3.1 73.1 - - + +
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Residues in contact with THR 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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105D PHE* 1.3 82.2 - - - +
107D CYS* 1.3 66.3 + - - +
108D LYS* 5.8 3.5 - - - +
161D THR* 5.9 3.4 - - - -
162D ALA 3.0 8.7 - - - -
163D ASN* 3.3 24.0 - - - +
1296D BOG 3.1 43.5 + - - +
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Residues in contact with CYS 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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85D VAL* 3.8 37.0 - - + -
105D PHE* 5.0 4.5 - - - -
106D THR* 1.3 77.6 - - - +
108D LYS* 1.3 66.7 + - - +
160D ILE 3.9 0.3 - - - +
161D THR* 3.4 1.6 - - - -
162D ALA* 2.6 56.6 + - - +
183D LEU* 5.1 13.9 - - - -
252D LEU* 4.8 12.8 - - - -
1296D BOG 4.7 8.7 - - - +
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Residues in contact with LYS 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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83D VAL* 5.6 5.4 - - - +
106D THR* 5.8 3.8 - - - +
107D CYS* 1.3 83.3 - - - +
109D ASN* 1.3 63.6 + - - +
159D GLU* 3.4 28.0 + - - +
160D ILE 3.3 5.2 - - - +
161D THR* 3.8 27.1 - - + +
183D LEU* 5.4 1.0 - - - +
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Residues in contact with ASN 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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83D VAL* 5.0 2.1 - - + +
108D LYS* 1.3 77.7 - - - +
110D THR* 1.3 66.7 + - - +
111D ASP* 3.0 27.5 + - - -
158D LYS 3.8 0.2 - - - +
159D GLU* 3.5 1.8 - - - +
160D ILE* 2.6 50.1 + - + +
183D LEU* 3.8 24.4 - - + +
185D LYS* 3.4 32.3 + - - +
249D GLY* 3.6 16.1 - - - +
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Residues in contact with THR 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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109D ASN* 1.3 83.9 + - - +
111D ASP* 1.3 74.4 + - - +
112D THR* 3.8 14.6 + - + +
157D SER* 3.8 19.5 - - - +
158D LYS 3.4 10.1 - - - +
159D GLU* 4.2 18.8 + - + +
185D LYS* 4.7 7.2 + - - +
247D VAL* 4.3 6.4 - - - +
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Residues in contact with ASP 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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109D ASN* 3.0 12.2 + - - -
110D THR* 1.3 72.8 - - - +
112D THR* 1.3 60.0 + - - +
138D THR* 4.3 18.2 + - - +
140D VAL* 4.9 5.8 - - + +
142D LEU* 4.0 7.9 - - + +
157D SER* 3.1 6.4 - - - -
158D LYS* 2.8 39.8 + - + +
160D ILE* 3.2 22.1 - - + +
247D VAL 3.2 7.0 - - - +
248D MET* 3.5 19.6 - - + +
249D GLY* 2.9 29.1 + - - +
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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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110D THR* 3.8 21.3 + - + +
111D ASP* 1.3 79.0 - - - +
113D VAL* 1.3 61.8 + - - +
142D LEU* 3.5 7.3 - - - +
156D ASN 3.5 7.0 - - - -
157D SER* 3.9 8.1 - - - -
245D SER 5.2 0.9 + - - -
246D ALA* 3.1 7.8 - - - +
247D VAL* 2.9 51.1 + - + +
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Residues in contact with VAL 113 (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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112D THR* 1.3 78.6 - - - +
114D THR* 1.3 70.8 + - - +
131D PHE* 4.9 1.1 - - + -
133D VAL* 3.7 28.3 - - + -
142D LEU* 3.7 20.6 - - + -
143D THR 4.4 3.1 - - - +
144D THR* 3.7 24.2 - - + +
154D ASN 4.5 0.2 - - - -
155D THR* 3.2 6.4 - - - -
156D ASN* 3.0 49.4 + - + +
244D TYR* 4.9 8.7 - - + -
245D SER 3.6 6.3 - - - +
246D ALA* 4.1 6.5 - - + -
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Residues in contact with THR 114 (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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113D VAL* 1.3 76.6 - - - +
115D ALA* 1.3 63.2 + - - +
116D THR* 4.5 1.7 + - - -
153D THR* 3.4 23.4 - - - +
154D ASN 3.4 4.3 - - - -
155D THR* 4.1 11.8 - - - +
244D TYR* 3.2 5.9 - - - +
245D SER* 3.0 48.7 + - - +
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Residues in contact with ALA 115 (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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113D VAL* 5.1 0.2 - - + -
114D THR* 1.3 76.1 + - - +
116D THR* 1.3 60.9 + - - +
131D PHE* 5.1 0.2 - - + -
144D THR* 4.0 19.7 - - - +
145D SER 4.3 6.2 - - - +
146D TYR* 3.6 31.0 - - + +
152D ASN 3.8 0.9 - - - +
153D THR* 3.2 2.9 - - - -
154D ASN* 2.8 42.1 + - - +
243D ASN 3.4 5.4 - - - -
244D TYR* 4.7 3.1 - - + -
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Residues in contact with THR 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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114D THR* 4.5 1.7 + - - -
115D ALA* 1.3 71.6 - - - +
117D THR* 1.3 74.3 + - - +
118D THR* 3.5 10.7 + - + +
146D TYR* 3.5 4.6 - - - -
151D THR 4.9 2.7 - - - +
152D ASN 3.3 6.1 - - - +
153D THR* 2.7 35.6 + - - +
242D GLY* 3.1 2.9 - - - -
243D ASN* 3.0 43.3 + - - +
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Residues in contact with THR 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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116D THR* 1.3 81.7 - - - +
118D THR* 1.3 60.3 + - - +
119D HIS 4.0 17.7 - - - +
120D THR* 4.0 9.2 - - + +
146D TYR* 3.6 16.7 - - - -
147D SER 2.8 28.3 + - - +
150D ASN 3.3 26.7 - - - +
151D THR* 3.4 19.4 - - - -
152D ASN 3.1 9.3 + - - -
194D LEU* 3.8 7.2 - - + +
241D LYS 3.7 12.6 - - - +
242D GLY* 4.1 1.8 - - - -
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Residues in contact with THR 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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116D THR* 3.5 13.9 + - + +
117D THR* 1.3 75.8 - - - +
119D HIS* 1.3 83.0 + - - +
120D THR 4.2 0.7 - - - -
151D THR* 4.3 10.7 - - - +
241D LYS* 3.0 27.7 + - - +
242D GLY* 3.3 4.0 + - - -
243D ASN* 3.8 28.5 - - - +
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Residues in contact with HIS 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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117D THR* 4.0 3.7 - - - +
118D THR* 1.3 101.3 + - - +
120D THR* 1.3 68.9 + - - +
151D THR* 5.3 0.2 - - - -
194D LEU* 4.9 0.2 - - - +
240D GLY* 3.2 4.0 - - - -
241D LYS* 2.9 60.3 + - + +
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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