Contacts of the strand formed by residues 129 - 132 (chain g) 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 ILE 129 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121g VAL* 3.7 27.4 - - + -
122g SER 4.2 7.9 - - - +
123g GLY* 5.0 0.2 - - - -
128g THR* 1.3 79.5 - - - +
130g LYS* 1.3 64.4 + - - +
142g VAL 2.8 14.6 - - - +
143g GLN* 3.3 1.4 - - - -
144g ASP* 3.0 38.8 + - + +
147g HIS* 4.2 13.0 - - + +
151g VAL* 4.5 15.0 - - + -
154g VAL* 4.6 5.8 - - + -
165g ILE* 5.0 5.6 - - + -
167g SER* 3.7 20.6 - - - +
177g TRP* 3.7 34.5 - - + +
179g LEU* 6.3 0.9 - - + -
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Residues in contact with LYS 130 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103g GLY* 3.6 25.1 + - - -
104g HIS* 3.9 25.4 + - + +
105g THR* 5.1 1.4 + - - -
121g VAL* 3.7 4.7 - - - +
122g SER 3.4 27.3 + - - -
126g ASP* 3.8 9.3 + - - -
128g THR* 3.3 23.7 + - - +
129g ILE* 1.3 81.6 - - - +
131g LEU* 1.3 62.3 + - - +
132g TRP* 3.6 32.3 + - + +
141g THR* 5.1 10.3 - - + -
142g VAL 3.2 6.1 - - - +
143g GLN* 4.3 27.1 - - + +
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Residues in contact with LEU 131 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119g GLN* 4.4 20.9 - - + -
120g ILE 3.4 11.9 - - - +
121g VAL* 4.6 3.8 - - + +
130g LYS* 1.3 73.9 - - - +
132g TRP* 1.3 79.3 + - - +
133g ASN* 4.4 1.9 + - + +
140g TYR* 3.9 41.6 - - + +
141g THR* 3.9 22.2 + - - +
142g VAL* 3.4 24.2 + - + +
179g LEU* 3.7 41.3 - - + -
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Residues in contact with TRP 132 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101g PHE* 3.8 47.5 - + + -
102g VAL 3.0 32.8 - - - -
104g HIS* 3.2 45.5 + + - -
119g GLN* 4.0 2.1 - - - -
120g ILE* 2.5 47.9 + - + +
122g SER* 3.3 13.1 + - - -
130g LYS* 3.6 35.2 - - + +
131g LEU* 1.3 83.6 - - - +
133g ASN* 1.3 60.5 + - - +
136g GLY 3.6 26.5 - - - -
137g VAL* 5.7 0.4 - - - -
141g THR* 6.3 4.0 - - + -
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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