Contacts of the strand formed by residues 134 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124F ASP 3.6 5.2 - - - +
125F VAL* 3.3 25.4 - - - +
126F SER 3.2 20.2 - - - +
128F VAL* 3.4 11.4 - - + +
133F GLY* 1.3 74.5 - - - -
135F THR* 1.3 62.4 + - - +
136F CYS 3.9 0.7 - - - -
199F LEU 3.5 1.1 - - - +
200F ASN* 2.8 15.6 + - - -
201F PHE* 2.8 37.7 + - + +
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Residues in contact with THR 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F ASP* 3.3 25.8 + - - +
126F SER 4.5 0.8 + - - -
133F GLY 4.2 1.3 + - - -
134F ALA* 1.3 70.3 - - - +
136F CYS* 1.3 61.5 + - - +
137F ARG* 3.7 10.3 + - + +
198F SER* 4.2 24.5 - - - +
199F LEU 3.2 8.5 - - - +
200F ASN* 3.1 24.3 + - + +
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Residues in contact with CYS 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F VAL* 3.8 15.0 - - + -
121F PHE* 4.9 0.4 - - - -
123F CYS* 2.0 47.3 - - - -
124F ASP 3.9 3.3 + - - +
134F ALA 3.9 0.4 - - - -
135F THR* 1.3 71.1 - - - +
137F ARG* 1.3 58.1 + - - +
138F ILE* 3.8 18.4 + - - +
197F VAL 3.5 2.6 - - - +
198F SER* 4.5 0.4 - - - -
199F LEU* 2.7 53.4 + - + +
201F PHE* 3.9 18.8 - - + -
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Residues in contact with ARG 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASN* 2.8 23.2 + - - -
123F CYS* 3.8 8.5 - - + +
124F ASP* 5.1 6.3 - - - +
135F THR* 3.7 11.3 + - + +
136F CYS* 1.3 74.5 - - - +
138F ILE* 1.3 62.3 + - - +
139F LYS* 4.1 1.0 + - - +
196F GLU* 3.8 35.7 + - + +
197F VAL 3.5 4.3 - - - +
198F SER* 3.4 23.6 - - - +
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 4.4 11.0 - - + -
35F PHE* 4.2 29.6 - - + -
50F VAL* 5.3 4.5 - - + -
52F PHE* 5.5 0.7 - - + -
88F ALA* 4.5 0.7 - - + -
90F ASN* 3.7 3.6 - - - +
121F PHE* 3.7 56.1 - - + -
136F CYS* 4.4 16.2 - - - +
137F ARG* 1.3 76.3 - - - +
139F LYS* 1.3 61.1 + - - +
140F ILE* 4.0 20.1 + - + -
195F VAL 3.5 2.1 - - - +
196F GLU* 3.4 4.4 - - - -
197F VAL* 2.8 47.0 + - + +
199F LEU* 5.6 1.1 - - + -
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ALA* 3.2 3.8 - - - -
89F TYR* 2.7 69.2 + - + +
90F ASN* 3.3 12.2 + - - +
137F ARG 4.1 1.3 + - - +
138F ILE* 1.3 72.0 - - - +
140F ILE* 1.3 60.4 + - - +
183F VAL* 4.8 5.9 - - - +
185F TYR* 2.8 34.6 + - - -
194F ASP* 3.3 34.4 + - - +
195F VAL 3.5 3.8 - - - -
196F GLU* 4.0 19.7 - - + +
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Residues in contact with ILE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 4.5 15.2 - - + +
33F LEU* 3.8 38.6 - - + -
52F PHE* 5.3 2.7 - - + -
54F GLN* 4.0 17.0 - - - +
86F LEU* 4.1 29.4 - - + -
87F ALA 3.2 10.1 - - - +
88F ALA* 4.2 11.9 - - + +
89F TYR* 4.6 0.2 - - - -
121F PHE* 6.3 0.2 - - + -
138F ILE* 4.1 15.0 - - + +
139F LYS* 1.3 79.4 - - - +
141F GLY* 1.3 61.4 + - - +
152F VAL* 4.6 2.1 - - - +
194F ASP* 3.2 3.9 - - - -
195F VAL* 2.7 44.7 + - + +
197F VAL* 5.4 3.4 - - + -
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Residues in contact with GLY 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F LEU* 3.3 11.8 - - - -
87F ALA* 3.0 29.8 + - - +
89F TYR* 3.9 11.5 - - - -
140F ILE* 1.3 77.4 - - - +
142F SER* 1.3 68.2 + - - -
143F TRP* 3.4 0.7 + - - -
152F VAL* 4.4 3.6 - - - -
193F GLU 3.5 16.6 - - - -
194F ASP* 4.0 1.3 - - - -
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Residues in contact with SER 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ASP* 2.6 29.1 + - - -
86F LEU* 3.7 8.4 - - - +
89F TYR* 3.6 13.5 + - - -
141F GLY* 1.3 73.9 - - - -
143F TRP* 1.3 61.6 + - - +
145F HIS* 3.0 38.4 + - - +
150F ILE* 4.0 22.4 - - - -
152F VAL* 4.4 2.2 - - - +
192F TYR* 4.5 8.9 - - - +
193F GLU 3.9 8.6 + - - +
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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