Contacts of the strand formed by residues 137 - 141 (chain E) in PDB entry 5FLX
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 PRO 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E ILE* 5.5 8.1 - - + -
130E THR 3.5 7.6 - - - +
131E VAL* 3.8 16.4 - - + -
135E GLY 4.0 3.8 - - - +
136E ILE* 1.3 86.4 - - - +
138E HIS* 1.3 66.1 + - - +
148E ARG* 3.7 1.7 - - - +
149E TYR* 3.1 45.9 + - + -
150E PRO* 3.9 7.9 - - + -
151E ASP 5.9 4.7 - - - +
152E PRO* 6.4 1.1 - - + -
209G TYR* 3.8 33.7 - - + +
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Residues in contact with HIS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231 G 4.2 15.9 + - - -
129E ILE* 3.3 11.8 - - - +
130E THR* 2.5 48.6 + - + +
131E VAL 4.1 0.4 - - - -
132E GLY* 3.4 21.5 + - - -
133E VAL 4.7 0.7 - - - -
136E ILE* 3.2 54.1 + - + +
137E PRO* 1.3 73.9 - - - +
139E LEU* 1.3 63.7 + - - +
140E VAL* 6.1 0.9 - - + -
146E THR* 4.7 13.9 - - + -
147E ILE 3.5 9.0 - - - +
148E ARG* 4.0 17.9 - - + +
150E PRO* 3.8 4.2 - - - +
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E CYS* 6.0 2.2 - - - -
126E VAL* 3.5 39.9 - - + -
128E LYS 3.8 3.8 - - - -
129E ILE* 4.6 5.8 - - + +
138E HIS* 1.3 75.5 - - - +
140E VAL* 1.3 86.9 + - - +
141E THR* 3.4 23.6 - - - +
145E ARG 3.7 0.3 - - - +
146E THR* 3.6 12.5 - - - +
147E ILE* 3.1 33.1 + - + -
150E PRO* 3.4 30.7 - - + -
154E ILE* 3.7 19.7 - - + -
160E VAL* 5.5 0.4 - - + -
169E ILE* 4.5 7.0 - - + -
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3431 A 3.2 31.4 - - + +
3441 U 4.7 1.6 - - - -
126E VAL* 3.4 5.9 - - - -
127E ARG* 2.5 58.5 + - + +
128E LYS* 2.8 44.0 + - + +
130E THR* 5.5 9.2 - - + -
138E HIS* 6.1 1.1 - - + -
139E LEU* 1.3 78.7 - - - +
141E THR* 1.3 62.4 + - - +
144E ALA* 5.8 2.0 - - - -
145E ARG 4.3 1.1 - - - -
146E THR* 5.4 5.2 - - + +
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3441 U 5.4 0.7 - - - +
124E CYS* 3.6 30.6 - - + -
125E LYS 3.3 14.0 + - - +
127E ARG* 4.0 9.9 + - - -
139E LEU* 3.4 15.8 - - - +
140E VAL* 1.3 75.3 - - - +
142E HIS* 1.3 63.0 + - - +
143E ASP* 3.3 18.2 - - + +
144E ALA* 2.7 24.8 + - - -
145E ARG* 3.1 37.2 + - + +
147E ILE* 5.6 0.5 - - - +
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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