Contacts of the strand formed by residues 134 - 142 (chain B) in PDB entry 3U8M
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 ALA 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASP 3.8 5.2 - - - +
125B VAL* 3.3 33.7 - - - +
126B SER 3.3 10.8 - - - +
128B VAL* 3.5 14.9 - - + +
133B GLY* 1.3 74.3 - - - -
135B THR* 1.3 59.0 + - - +
136B CYS 4.0 0.4 - - - -
199B LEU 3.5 1.0 - - - +
200B ASN* 2.7 18.5 + - - -
201B PHE* 2.7 35.6 + - + -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.3 25.2 + - - +
126B SER 4.6 1.2 + - - -
133B GLY 4.2 0.9 + - - -
134B ALA* 1.3 71.5 - - - +
136B CYS* 1.3 62.4 + - - +
137B ARG* 3.8 4.4 + - + +
198B SER* 4.2 26.2 - - - +
199B LEU 3.4 6.5 - - - +
200B ASN* 3.2 23.8 + - + +
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL* 3.9 13.0 - - + -
50B VAL* 6.0 0.4 - - - -
123B CYS* 2.0 48.7 - - - -
124B ASP 3.9 4.5 - - - +
134B ALA 4.0 0.6 - - - -
135B THR* 1.3 71.4 - - - +
137B ARG* 1.3 59.1 + - - +
138B ILE* 3.7 18.3 + - - +
197B VAL 3.5 2.8 - - - +
198B SER* 4.6 0.9 - - - -
199B LEU* 2.8 48.2 + - + +
201B PHE* 3.9 18.2 - - + -
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Residues in contact with ARG 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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90B ASN* 2.9 21.8 + - - -
123B CYS* 3.9 8.5 - - + +
124B ASP 5.0 0.6 - - - +
135B THR* 3.8 7.5 + - + +
136B CYS* 1.3 72.8 - - - +
138B ILE* 1.3 63.1 + - - +
139B LYS* 4.1 4.3 + - - +
196B GLU* 3.4 44.0 + - + +
197B VAL 3.6 3.6 - - - +
198B SER* 4.2 18.6 - - - +
167C GLN* 3.7 18.4 + - - +
168C TYR* 3.3 35.6 + - + +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.6 6.3 - - + -
35B PHE* 4.5 26.5 - - + -
50B VAL* 5.3 4.0 - - + -
52B PHE* 5.6 0.2 - - + -
88B ALA* 4.5 0.9 - - + -
90B ASN* 3.7 4.5 - - - +
121B PHE* 3.5 59.2 - - + -
136B CYS* 4.3 16.8 - - - +
137B ARG* 1.3 76.3 - - - +
139B LYS* 1.3 60.9 + - - +
140B ILE* 3.9 22.8 + - + +
195B VAL 3.5 1.9 - - - +
196B GLU* 3.5 2.7 - - - -
197B VAL* 2.9 47.9 + - + +
199B LEU* 5.6 2.5 - - + -
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Residues in contact with LYS 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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88B ALA* 3.2 4.3 - - - -
89B TYR* 2.7 67.6 + - + -
90B ASN* 3.3 10.5 + - - +
137B ARG* 4.1 4.4 + - - +
138B ILE* 1.3 71.0 - - - +
140B ILE* 1.3 60.8 + - - +
183B VAL* 4.6 7.5 - - - +
185B TYR* 2.9 29.0 + - - -
194B ASP* 3.3 38.5 + - - +
195B VAL 3.6 3.4 - - - -
196B GLU* 4.0 20.0 - - + +
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Residues in contact with ILE 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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31B VAL* 4.6 13.8 - - + +
33B LEU* 4.0 33.4 - - + -
52B PHE* 5.2 3.4 - - + -
54B GLN* 4.0 21.5 - - - +
86B LEU* 4.1 28.5 - - + -
87B ALA 3.2 11.2 - - - +
88B ALA* 4.1 13.0 - - + -
138B ILE* 4.0 15.0 - - + +
139B LYS* 1.3 79.0 - - - +
141B GLY* 1.3 59.4 + - - +
152B VAL* 4.6 2.4 - - - +
194B ASP* 3.3 4.2 - - - -
195B VAL* 2.8 44.8 + - + +
197B VAL* 5.4 2.7 - - + -
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Residues in contact with GLY 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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86B LEU* 3.3 10.0 - - - -
87B ALA* 2.9 30.6 + - - +
89B TYR* 4.0 10.2 - - - -
140B ILE* 1.3 78.1 - - - +
142B SER* 1.3 66.2 + - - -
152B VAL* 4.6 3.6 - - - -
193B GLU 3.6 16.4 - - - -
194B ASP* 4.0 3.6 - - - -
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 2.6 27.8 + - - -
86B LEU* 3.7 8.2 - - - +
89B TYR* 3.6 13.9 + - - -
141B GLY* 1.3 73.8 - - - -
143B TRP* 1.3 61.2 + - - +
145B HIS* 3.0 37.4 + - - +
150B ILE* 4.1 23.8 - - - -
152B VAL* 4.6 2.0 - - - +
192B TYR* 4.5 8.7 - - - +
193B GLU 3.9 8.8 + - - +
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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