Contacts of the strand formed by residues 128 - 143 (chain A) in PDB entry 5W30
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 VAL 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU 3.6 1.0 - - - +
124A THR* 3.2 3.2 - - - -
125A ILE 2.9 45.6 + - - +
126A ALA* 3.1 6.4 + - + +
127A GLY* 1.3 79.8 - - - +
129A SER* 1.3 66.3 + - - +
163A ASP 4.6 4.9 - - - +
164A PHE* 3.0 50.2 - - + +
165A LYS* 5.5 8.1 - - + +
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Residues in contact with SER 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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122A THR* 4.0 14.7 - - - +
123A LEU 3.2 4.5 - - - -
124A THR* 2.5 31.0 + - - +
127A GLY 4.0 2.6 + - - -
128A VAL* 1.3 79.5 - - - +
130A LYS* 1.3 62.2 + - - +
163A ASP 5.7 0.2 - - - +
164A PHE* 4.7 0.2 - - - -
302A SO4 4.2 7.9 + - - -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 3.5 1.9 - - - -
123A LEU* 2.8 36.5 + - - +
129A SER* 1.3 75.8 - - - +
131A ASP* 1.3 77.5 + - - +
132A ILE* 3.8 9.2 + - + +
163A ASP* 4.1 40.7 + - + +
164A PHE* 3.8 21.9 - - + -
302A SO4 3.1 30.2 + - - +
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Residues in contact with ASP 131 (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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107A LYS* 3.3 24.9 + - - +
120A THR* 4.7 13.1 - - + +
121A GLY 3.1 8.5 - - - +
122A THR* 2.6 30.9 + - - +
130A LYS* 1.3 88.4 - - - +
132A ILE* 1.3 62.6 + - - +
302A SO4 3.0 26.8 + - - +
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Residues in contact with ILE 132 (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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104A PHE* 3.9 17.2 - - + -
119A MET 3.6 0.7 - - - +
120A THR* 3.3 7.6 - - - +
121A GLY 2.8 38.5 + - - +
123A LEU* 4.0 26.2 - - + -
130A LYS* 4.0 13.7 - - + +
131A ASP* 1.3 80.3 - - - +
133A VAL* 1.3 63.1 + - - +
134A LEU* 3.9 29.2 - - + -
158A LYS 5.9 0.2 - - - +
159A ILE* 3.9 27.6 - - + -
164A PHE* 4.3 14.6 - - + -
181A LEU* 4.1 4.5 - - + -
301A UNL 5.7 0.4 - - + -
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Residues in contact with VAL 133 (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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118A LYS* 4.3 34.3 - - + +
119A MET 3.2 5.2 - - - +
120A THR* 3.6 24.9 - - + +
132A ILE* 1.3 76.2 - - - +
134A LEU* 1.3 68.6 + - - +
135A ASP* 5.7 4.8 - - - +
157A GLY* 4.2 10.0 - - - -
158A LYS 5.2 2.6 + - - +
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Residues in contact with LEU 134 (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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104A PHE* 4.1 29.8 - - + -
118A LYS* 3.8 4.9 - - - +
119A MET* 2.8 43.4 + - + +
132A ILE* 3.9 13.9 - - + -
133A VAL* 1.3 81.4 - - - +
135A ASP* 1.3 65.2 + - - +
136A ALA 3.6 0.6 + - - -
155A LEU* 4.1 35.2 - - + -
156A ASN 3.4 4.5 - - - +
157A GLY* 4.0 17.3 - - - +
159A ILE* 5.8 0.2 - - + -
181A LEU* 3.9 29.8 - - + -
183A ILE* 5.3 4.7 - - + -
301A UNL 5.4 4.7 - - + -
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Residues in contact with ASP 135 (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 ILE* 5.8 2.6 - - - +
117A GLY 4.0 5.6 - - - +
118A LYS* 4.8 11.1 - - - +
133A VAL* 5.7 5.0 - - - +
134A LEU* 1.3 75.8 - - - +
136A ALA* 1.3 63.1 + - - +
137A GLU* 3.7 1.6 + - - +
154A SER 3.3 6.8 - - - +
155A LEU* 4.4 1.3 - - - -
156A ASN* 2.6 47.5 + - + +
157A GLY* 5.4 1.7 - - - -
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Residues in contact with ALA 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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65A PHE* 4.7 8.5 - - + -
109A TYR* 3.6 29.2 - - + +
116A LYS* 3.3 6.6 - - - +
117A GLY 2.9 39.6 + - - +
119A MET* 5.0 2.9 - - + +
134A LEU 3.6 2.7 + - - +
135A ASP* 1.3 72.7 - - - +
137A GLU* 1.3 59.8 + - - +
138A ILE* 4.2 1.3 - - + -
153A PHE* 6.0 0.7 - - + -
154A SER 3.3 7.2 - - - +
155A LEU* 3.8 15.9 - - + -
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Residues in contact with GLU 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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115A GLU* 3.2 10.8 - - + +
116A LYS* 3.6 25.8 - - - +
135A ASP 3.7 2.4 + - - +
136A ALA* 1.3 73.9 - - - +
138A ILE* 1.3 68.0 + - - +
139A GLY* 3.4 1.5 + - - -
153A PHE* 3.4 2.2 - - - +
154A SER* 2.8 49.5 + - - +
156A ASN* 5.4 3.2 + - - +
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Residues in contact with ILE 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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58A PHE* 4.4 25.4 - - + -
63A ALA* 4.8 4.5 - - + +
65A PHE* 4.5 10.3 - - + -
109A TYR* 4.0 20.9 - - - +
114A ASN 3.7 27.4 - - - +
115A GLU* 2.7 32.2 + - + +
116A LYS* 5.3 0.2 - - - -
136A ALA* 5.5 1.6 - - + -
137A GLU* 1.3 73.6 - - - +
139A GLY* 1.3 61.2 + - - +
140A GLY* 3.4 17.0 - - - +
141A VAL* 3.9 22.2 - - + -
151A ILE* 6.2 0.2 - - + -
152A GLY 4.0 5.6 - - - +
153A PHE* 4.1 11.4 - - + -
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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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137A GLU* 3.4 7.3 + - - -
138A ILE* 1.3 72.0 - - - +
140A GLY* 1.4 54.8 + - - -
152A GLY* 2.8 21.9 + - - -
153A PHE* 3.8 1.3 - - - +
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Residues in contact with GLY 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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138A ILE* 3.3 9.9 - - - +
139A GLY* 1.4 78.8 - - - +
141A VAL* 1.3 64.1 + - - -
142A ALA* 3.8 3.9 + - - +
150A LYS* 4.8 0.7 - - - +
151A ILE* 3.6 3.3 - - - -
152A GLY* 3.2 24.2 + - - -
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Residues in contact with VAL 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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58A PHE* 3.8 25.1 - - + -
60A PRO* 3.8 30.1 - - + +
63A ALA* 5.8 3.1 - - + -
138A ILE* 3.9 19.0 - - + +
140A GLY* 1.3 73.1 - - - -
142A ALA* 1.3 61.4 + - - +
149A GLU* 4.1 11.2 - - - +
150A LYS 4.1 3.1 - - - -
151A ILE* 3.9 14.8 - - + -
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Residues in contact with ALA 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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140A GLY 3.8 4.5 + - - +
141A VAL* 1.3 75.2 - - - +
143A LYS* 1.3 61.8 + - - +
149A GLU* 3.2 13.1 - - - +
150A LYS* 3.0 55.9 + - + +
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Residues in contact with LYS 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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142A ALA* 1.3 75.4 - - - +
144A GLY* 1.3 68.2 + - - +
145A LYS* 5.5 0.2 + - - -
147A GLY* 3.7 29.4 - - - +
148A LYS 4.1 1.1 - - - -
149A GLU* 3.8 30.9 + - - +
150A LYS* 4.7 1.2 - - - -
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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