Contacts of the strand formed by residues 132 - 142 (chain B) in PDB entry 4U9W
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 ASP 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.1 4.3 - - - +
128B VAL* 3.2 5.2 - - - -
129B GLU 2.8 35.2 + - - +
130B CYS* 4.1 8.4 - - - +
131B GLY* 1.3 84.4 - - - +
133B GLU* 1.3 67.2 + - - +
134B VAL* 3.5 12.4 + - + +
169B LYS* 3.7 28.0 - - + +
170B LYS* 4.1 18.4 + - - -
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 5.3 0.2 - - - -
25B VAL* 3.4 35.4 + - - +
28B LYS* 3.8 27.5 + - + +
29B VAL* 3.7 22.9 - - + -
127B ASP 3.6 5.8 - - - -
132B ASP* 1.3 74.7 - - - +
134B VAL* 1.3 62.7 + - - +
167B GLN 3.7 21.2 - - - +
168B MET* 3.9 12.3 - - + -
169B LYS* 2.8 60.3 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 3.6 0.3 - - - -
127B ASP* 2.9 43.4 + - + +
129B GLU* 4.0 20.9 - - + -
132B ASP* 3.7 19.3 - - + +
133B GLU* 1.3 80.4 - - - +
135B LEU* 1.3 59.5 - - - +
136B TYR* 4.1 13.9 - - + +
168B MET* 3.5 12.9 - - - +
170B LYS* 3.6 31.4 - - + +
172B MET* 3.7 26.9 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.5 41.7 - - + -
125B ARG 3.3 8.1 - - - +
126B PHE* 3.9 18.6 - - + +
134B VAL* 1.3 74.0 - - - +
136B TYR* 1.3 61.7 + - - +
137B CYS 3.7 2.1 + - - +
159B LEU* 3.3 43.3 - - + +
162B MET* 4.0 8.5 - - + -
163B ALA* 3.7 25.8 - - + +
168B MET* 3.7 6.9 - - + +
170B LYS 3.0 7.7 + - - +
171B VAL* 3.2 8.1 - - + -
172B MET 3.0 23.2 + - - -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.1 5.5 - - - +
125B ARG* 2.7 40.7 + - + +
127B ASP* 5.1 1.6 - - + -
129B GLU* 4.7 2.2 - - + -
134B VAL* 3.7 10.5 - - + -
135B LEU* 1.3 73.3 - - - +
137B CYS* 1.3 70.0 + - - +
138B TYR* 3.4 28.1 + + + -
172B MET* 3.5 39.3 - - + -
173B LEU* 3.6 11.5 + - - -
174B THR* 2.6 29.8 + - - -
213B ILE* 4.1 6.1 - - - +
2E GLY 3.5 20.0 - - - -
3E ARG* 3.5 48.7 - - + +
4E GLY 4.0 1.8 + - - -
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Residues in contact with CYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER* 3.7 2.2 - - - -
123B HIS 3.9 2.0 - - - -
124B PHE* 4.3 3.4 - - - -
135B LEU* 3.7 2.4 + - - +
136B TYR* 1.3 75.1 - - - +
138B TYR* 1.3 60.3 + - - +
139B GLU 3.4 27.6 - - - -
140B VAL* 4.4 5.6 - - - -
156B ILE* 4.3 14.4 - - + -
159B LEU* 3.6 30.1 - - + -
171B VAL* 4.4 8.5 - - + -
172B MET 2.8 15.6 + - - +
173B LEU* 3.2 33.1 - - + +
174B THR 4.5 0.2 + - - -
186B PHE* 5.4 0.4 - - - -
1E SER 5.0 1.9 + - - -
2E GLY 4.3 1.9 - - - +
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLU* 3.7 33.9 - - + -
123B HIS* 2.8 40.4 + + - +
125B ARG* 3.5 45.2 + - + -
136B TYR* 3.6 29.4 - + + -
137B CYS* 1.3 72.1 - - - +
139B GLU* 1.3 65.4 + - - +
1E SER* 3.1 5.6 - - - -
2E GLY 2.7 39.6 + - - -
3E ARG* 2.8 45.7 + - + +
101E NA 4.5 0.2 - - - -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 3.6 15.7 - - - +
97B LYS* 3.0 24.3 + - - +
100B GLU* 4.1 2.9 - - - +
101B MET* 4.9 3.5 - - + +
121B PHE* 3.9 15.3 - - + -
122B SER* 2.9 24.1 + - - -
123B HIS* 3.0 31.7 + - + -
137B CYS* 3.4 6.6 - - - -
138B TYR* 1.3 90.0 - - - +
140B VAL* 1.3 58.8 + - - +
141B GLN* 3.5 28.4 + - + -
1E SER* 2.2 34.2 + - - -
101E NA 3.6 4.7 - - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PHE 3.3 9.2 - - - +
122B SER* 4.4 3.1 - - - -
137B CYS* 4.4 3.8 - - - -
139B GLU* 1.3 75.4 - - - +
141B GLN* 1.3 64.6 + - - +
142B LEU* 4.1 10.5 - - + -
152B GLY 4.8 4.0 - - - +
155B LEU* 4.2 16.4 - - + -
156B ILE* 4.2 22.4 - - + -
186B PHE* 3.8 29.6 - - + -
301B COA 2.9 51.9 + - + +
101E NA 3.3 10.2 - - - -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.6 12.5 - - + +
77B THR* 3.9 9.0 - - - +
80B ASN* 2.7 39.7 + - - +
81B MET* 3.4 29.7 - - - +
120B ALA* 3.2 3.5 - - - -
121B PHE* 2.9 62.5 + - + -
139B GLU* 3.5 28.0 + - + +
140B VAL* 1.3 85.0 + - - +
142B LEU* 1.3 62.7 + - - +
301B COA 3.2 10.9 + - - +
101E NA 4.0 4.2 - - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.8 5.2 - - - +
80B ASN* 3.6 5.7 + - - +
119B VAL 3.6 3.4 - - - -
120B ALA* 3.7 17.3 - - + -
140B VAL* 4.1 12.8 - - + -
141B GLN* 1.3 82.8 - - - +
143B GLU* 1.3 70.5 + - - +
146B VAL* 3.9 22.9 - - + +
147B ARG* 3.1 28.0 + - + -
151B LEU* 4.1 7.0 - - + -
152B GLY* 3.8 14.4 - - - +
155B LEU* 4.3 3.6 - - + -
301B COA 2.9 64.2 + - + +
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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