Contacts of the strand formed by residues 105 - 119 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL* 4.1 17.3 - - + -
103A GLN* 3.6 15.9 - - + +
104A SER* 1.3 75.6 - - - +
106A THR* 1.3 78.2 + - - +
107A CYS* 4.9 3.1 - - - -
163A ASN* 3.7 0.7 - - - -
164A VAL* 2.8 74.5 + - + +
165A PRO 5.0 1.3 - - - -
181A ALA* 4.1 18.2 - - + -
252A LEU* 4.6 8.1 - - + -
254A VAL* 5.4 1.8 - - + -
1297A BOG 3.2 72.7 - - + +
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Residues in contact with THR 106 (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 PHE* 1.3 82.8 - - - +
107A CYS* 1.3 66.3 + - - +
108A LYS* 5.8 2.2 - - - +
161A THR* 4.6 9.9 - - + -
162A ALA 3.0 9.6 - - - -
163A ASN* 3.3 23.8 - - - +
1297A BOG 3.1 43.4 + - - +
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Residues in contact with CYS 107 (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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85A VAL* 3.8 37.7 - - + -
105A PHE* 4.9 4.3 - - - -
106A THR* 1.3 77.8 - - - +
108A LYS* 1.3 66.8 + - - +
160A ILE 3.9 0.5 - - - +
161A THR* 3.4 2.0 - - - +
162A ALA* 2.6 54.5 + - - +
183A LEU* 5.2 13.7 - - - -
252A LEU* 4.8 13.0 - - - -
1297A BOG 5.0 8.1 - - - +
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Residues in contact with LYS 108 (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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83A VAL* 5.7 5.2 - - - +
106A THR* 5.8 2.2 - - - +
107A CYS* 1.3 81.9 - - - +
109A ASN* 1.3 63.8 + - - +
159A GLU* 3.6 30.2 + - + +
160A ILE 3.3 5.6 - - - +
161A THR* 3.8 26.1 + - + +
183A LEU* 5.4 1.0 - - - +
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Residues in contact with ASN 109 (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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83A VAL* 5.0 2.1 - - + +
108A LYS* 1.3 77.9 - - - +
110A THR* 1.3 65.1 + - - +
111A ASP* 3.0 28.3 + - - -
159A GLU* 3.5 2.0 - - - +
160A ILE* 2.6 50.0 + - + +
183A LEU* 3.8 24.9 - - + +
185A LYS* 3.4 32.4 + - - +
249A GLY* 3.6 15.7 - - - +
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Residues in contact with THR 110 (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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109A ASN* 1.3 85.9 + - - +
111A ASP* 1.3 72.0 + - - +
112A THR* 3.8 14.8 + - + +
157A SER* 3.8 20.0 - - - +
158A LYS 3.4 9.2 - - - +
159A GLU* 4.2 16.8 + - + +
185A LYS* 4.7 7.3 + - - +
247A VAL* 4.3 6.4 - - - +
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Residues in contact with ASP 111 (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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109A ASN* 3.0 13.0 + - - +
110A THR* 1.3 72.7 - - - +
112A THR* 1.3 59.4 + - - +
138A THR* 4.3 17.8 + - - +
140A VAL* 4.8 5.6 - - + +
142A LEU* 4.0 7.4 - - + +
157A SER* 3.1 6.9 - - - -
158A LYS* 2.8 40.5 + - + +
160A ILE* 3.2 22.5 - - + +
247A VAL 3.2 7.6 - - - +
248A MET* 3.5 19.7 - - + +
249A GLY* 2.9 29.7 + - - +
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Residues in contact with THR 112 (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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110A THR* 3.8 22.6 + - + +
111A ASP* 1.3 79.4 - - - +
113A VAL* 1.3 64.6 + - - +
142A LEU* 3.5 6.6 - - - +
156A ASN 3.4 6.3 - - - +
157A SER* 3.9 8.5 - - - -
245A SER 5.2 0.7 + - - -
246A ALA* 3.1 8.0 - - - +
247A VAL* 2.9 50.6 + - + +
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Residues in contact with VAL 113 (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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112A THR* 1.3 78.4 - - - +
114A THR* 1.3 70.1 + - - +
131A PHE* 4.9 7.4 - - + -
133A VAL* 3.7 28.3 - - + -
142A LEU* 3.7 20.0 - - + -
143A THR 4.4 3.4 - - - +
144A THR* 3.9 25.8 - - + -
155A THR* 3.2 6.4 - - - -
156A ASN* 3.0 49.9 + - + +
244A TYR* 4.9 2.0 - - + -
245A SER 3.6 6.1 - - - +
246A ALA* 4.2 5.6 - - + -
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Residues in contact with THR 114 (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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113A VAL* 1.3 77.1 - - - +
115A ALA* 1.3 64.2 + - - +
116A THR* 4.5 1.6 + - - -
153A THR* 3.4 23.0 - - - +
154A ASN 3.4 4.7 + - - -
155A THR* 4.1 11.1 - - - +
244A TYR* 3.2 6.2 - - - +
245A SER* 3.0 48.3 + - - +
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Residues in contact with ALA 115 (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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114A THR* 1.3 76.1 + - - +
116A THR* 1.3 62.7 + - - +
144A THR* 3.5 27.1 - - + -
145A SER 4.2 7.5 - - - +
146A TYR* 3.6 27.8 - - + +
152A ASN 3.8 0.9 - - - +
153A THR* 3.2 2.6 - - - -
154A ASN* 2.8 37.6 + - - +
243A ASN 3.4 5.8 - - - -
244A TYR* 4.6 2.5 - - + -
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Residues in contact with THR 116 (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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114A THR* 4.5 1.7 + - - -
115A ALA* 1.3 70.3 - - - +
117A THR* 1.3 73.5 + - - +
118A THR* 3.5 10.7 + - + +
146A TYR* 3.5 4.1 - - - -
151A THR* 4.9 3.4 - - - +
152A ASN 3.2 6.7 - - - +
153A THR* 2.7 33.9 + - - +
242A GLY* 3.1 3.1 - - - -
243A ASN* 3.0 43.9 + - - +
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Residues in contact with THR 117 (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 THR* 1.3 80.9 - - - +
118A THR* 1.3 58.6 + - - +
119A HIS 4.0 18.4 - - - +
120A THR* 4.0 10.5 - - + +
146A TYR* 3.6 12.4 - - - -
147A SER* 2.8 33.4 + - - +
150A ASN 3.3 23.3 - - - +
151A THR* 3.5 21.1 - - - +
152A ASN 3.1 9.4 + - - -
194A LEU* 3.8 6.7 - - + +
241A LYS 3.7 13.0 - - - +
242A GLY* 4.1 1.3 - - - -
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Residues in contact with THR 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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116A THR* 3.5 14.1 + - + +
117A THR* 1.3 76.2 - - - +
119A HIS* 1.3 83.9 + - - +
120A THR 4.2 0.7 - - - -
151A THR* 4.3 10.3 - - - +
241A LYS* 3.0 27.0 + - - +
242A GLY* 3.3 4.7 + - - -
243A ASN* 3.8 27.8 - - - +
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Residues in contact with HIS 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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117A THR* 4.0 4.4 - - - +
118A THR* 1.3 101.8 + - - +
120A THR* 1.3 69.5 + - - +
151A THR* 5.3 0.7 - - - -
194A LEU* 4.9 0.3 - - - +
240A GLY* 3.2 3.5 - - - -
241A LYS* 2.9 57.3 + - + +
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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