Contacts of the strand formed by residues 135 - 146 (chain A) in PDB entry 1WZN
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 LEU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASN* 3.1 25.9 + - - -
106A PHE 3.5 14.4 - - - +
107A ASP 3.9 1.1 - - - +
108A ALA* 3.8 7.4 - - - -
109A VAL* 3.6 19.3 - - + -
131A VAL* 3.2 14.8 + - + +
132A ALA* 3.3 10.7 + - - +
134A ALA* 1.3 78.5 - - - +
136A LYS* 1.3 67.9 + - - +
137A PRO 4.0 0.2 - - - -
139A GLY 4.0 10.1 - - - +
140A VAL 3.6 39.3 - - - +
141A PHE 4.1 0.4 - - - +
223A PHE* 3.8 29.6 - - + -
249A ALA* 4.2 10.5 - - + -
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Residues in contact with LYS 136 (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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40A ARG* 3.4 28.6 - - - +
44A ARG* 5.5 4.4 - - - +
104A ASN 3.6 19.1 - - - +
105A GLU* 3.6 24.7 - - - +
106A PHE 2.9 20.4 + - - +
107A ASP* 3.2 28.0 + - - +
135A LEU* 1.3 78.6 - - - +
137A PRO* 1.3 75.8 - - + +
138A GLY 3.3 0.3 + - - -
139A GLY* 2.8 16.5 + - - -
249A ALA* 3.9 2.4 - - - +
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Residues in contact with PRO 137 (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 LYS 4.8 0.5 - - - +
40A ARG* 2.8 37.6 + - - +
104A ASN* 5.3 7.2 - - + +
135A LEU 4.5 1.6 - - - +
136A LYS* 1.3 86.5 - - + +
138A GLY* 1.3 58.6 + - - +
249A ALA* 4.7 2.0 - - + -
250A LYS 3.4 15.3 - - - +
251A SER* 4.0 15.0 - - - -
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Residues in contact with GLY 138 (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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38A ALA* 3.7 3.3 - - - -
39A LYS* 2.8 39.3 + - - +
40A ARG* 3.8 5.7 - - - +
136A LYS 3.3 0.6 + - - -
137A PRO* 1.3 71.5 - - - +
139A GLY* 1.3 65.4 + - - +
140A VAL* 4.2 0.5 - - - +
248A ILE* 4.3 1.7 - - - +
249A ALA 3.2 24.0 + - - -
250A LYS 3.2 3.6 + - - -
251A SER* 3.6 14.5 - - - -
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Residues in contact with GLY 139 (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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38A ALA* 5.2 0.7 - - - -
40A ARG* 3.8 8.3 - - - -
107A ASP 3.1 18.6 - - - -
135A LEU* 4.0 8.6 - - - +
136A LYS 2.8 17.1 + - - -
137A PRO 3.1 1.4 + - - -
138A GLY* 1.3 81.3 - - - +
140A VAL* 1.3 60.7 + - - +
247A GLY 3.9 0.2 - - - +
249A ALA* 2.9 26.0 + - - +
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Residues in contact with VAL 140 (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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33A ILE* 4.8 3.1 - - + -
34A PHE* 4.0 21.8 - - + -
37A ASP* 4.1 4.9 - - + -
38A ALA* 3.4 38.8 - - + +
42A VAL* 5.0 0.2 - - + -
107A ASP 3.1 6.0 + - - +
108A ALA* 3.1 20.7 - - + +
109A VAL 2.8 25.3 + - - +
135A LEU* 3.6 6.5 - - - +
138A GLY 4.2 0.7 - - - +
139A GLY* 1.3 77.1 - - - +
141A PHE* 1.3 58.9 + - - +
142A ILE* 4.2 9.6 - - + +
246A VAL* 4.5 10.8 - - + -
247A GLY 3.2 9.4 - - - +
248A ILE* 4.1 11.9 - - + -
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Residues in contact with PHE 141 (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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48A LEU* 5.0 1.6 - - + -
109A VAL* 3.2 22.9 - - + +
111A MET* 4.3 13.5 - - + -
116A ILE* 5.1 2.5 - - + -
127A LEU* 5.2 5.2 - - + -
128A PHE* 3.5 34.1 - + - -
131A VAL* 3.6 40.6 - - + -
135A LEU* 4.1 0.4 - - + +
140A VAL* 1.3 73.4 - - - +
142A ILE* 1.3 71.9 + - - +
143A THR* 3.7 31.4 - - + -
219A ALA* 6.1 0.2 - - + -
223A PHE* 3.7 30.7 - + + -
245A ILE* 3.6 8.4 - - + +
246A VAL* 3.2 7.3 - - - +
247A GLY 2.8 34.5 + - - +
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Residues in contact with ILE 142 (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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30A VAL* 4.0 14.8 - - + -
33A ILE* 3.6 43.5 - - + -
34A PHE* 3.6 32.1 - - + -
108A ALA* 5.6 0.2 - - + -
109A VAL 2.9 8.6 + - - +
110A THR* 3.3 13.7 - - + -
111A MET 3.0 23.2 + - - +
112A PHE* 4.9 2.6 - - + -
140A VAL* 4.2 7.2 - - + -
141A PHE* 1.3 80.9 - - - +
143A THR* 1.3 63.9 - - - +
244A TRP* 3.5 30.7 - - + -
245A ILE 3.5 5.6 - - - +
246A VAL* 4.4 4.9 - - + -
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Residues in contact with THR 143 (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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111A MET* 2.7 29.0 + - - +
112A PHE* 5.9 0.2 - - - -
115A THR 5.5 0.2 + - - -
116A ILE* 3.7 30.8 + - + +
128A PHE* 5.3 1.8 - - + -
141A PHE* 3.7 30.5 - - + -
142A ILE* 1.3 77.0 - - - +
144A ASP* 1.3 63.1 + - - +
145A PHE* 4.4 1.5 - - + -
215A VAL* 5.4 0.9 - - + -
243A TYR 4.0 0.2 - - - +
244A TRP* 3.4 6.4 - - - -
245A ILE* 2.9 46.5 + - + -
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Residues in contact with ASP 144 (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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19A ARG* 5.5 0.5 + - - -
26A GLU* 5.0 1.4 - - - +
112A PHE* 3.3 15.6 - - - -
113A PHE* 2.8 40.2 + - - -
114A SER* 2.9 27.2 + - - -
116A ILE* 5.1 0.5 - - - +
143A THR* 1.3 81.4 + - - +
145A PHE* 1.3 63.8 + - - +
242A ARG* 3.2 27.9 + - + +
243A TYR 3.1 11.9 - - - +
244A TRP* 3.6 26.2 - - + -
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Residues in contact with PHE 145 (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 SER* 4.0 4.5 - - - -
116A ILE* 3.6 30.1 - - + -
117A MET* 5.0 5.4 - - + -
143A THR* 4.4 2.5 - - + -
144A ASP* 1.3 81.1 - - - +
146A PRO* 1.3 81.7 - - + +
210A TYR* 4.1 18.8 - - + -
212A PRO* 4.0 16.2 - - + -
215A VAL* 3.5 26.0 - - + -
242A ARG* 3.7 5.5 - - - +
243A TYR* 2.8 64.3 + + + +
245A ILE* 3.3 32.8 - - + -
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Residues in contact with PRO 146 (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 SER* 3.0 26.5 - - - +
117A MET* 4.0 19.7 - - + +
145A PHE* 1.3 102.9 - - + +
147A CYS* 1.3 70.0 + - - +
210A TYR 4.8 4.2 - - - +
241A MET 3.7 7.9 - - - +
242A ARG* 4.4 8.7 - - + -
243A TYR* 4.2 3.2 - - - -
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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