Contacts of the strand formed by residues 300 - 303 (chain C) in PDB entry 5IWG
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 LEU 300 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU* 3.8 7.4 - - - +
135C ASP 3.1 6.1 + - - -
136C MET* 3.3 31.8 - - + +
137C ALA 3.0 25.1 + - - +
262C VAL* 3.3 13.5 - - + +
264C LEU* 4.0 21.1 - - + -
290C VAL* 5.2 2.5 - - + -
293C VAL* 3.8 31.2 - - + +
294C LYS* 4.2 18.8 - - + +
298C LEU 3.7 9.4 - - - +
299C PRO* 1.3 74.5 - - - +
301C LEU* 1.3 63.3 + - - +
302C MET* 3.9 22.2 + - + -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLY 5.1 0.9 - - - +
122C SER* 3.8 10.1 - - - +
125C GLY* 4.0 15.3 - - - -
126C ALA* 4.6 7.0 - - + +
129C LEU* 3.9 10.0 - - + +
137C ALA* 3.4 30.3 - - + +
138C VAL 4.9 0.4 - - - +
139C ASN* 5.3 1.6 - - + +
164C ALA* 3.7 29.6 - - + -
168C LEU* 4.8 3.6 - - + -
262C VAL 2.9 12.6 + - - +
263C VAL* 3.4 23.2 - - + +
264C LEU 2.9 28.1 + - - +
300C LEU* 1.3 71.4 - - - +
302C MET* 1.3 59.9 + - - +
303C LEU* 3.7 26.2 - - + -
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Residues in contact with MET 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C MET* 4.7 4.0 - - - +
137C ALA 2.8 13.1 + - - +
138C VAL* 3.4 14.0 - - + +
139C ASN 2.9 27.0 + - - -
140C TRP* 3.5 31.6 - - + -
264C LEU* 3.5 15.3 - - + +
266C CYS* 4.7 1.6 - - - -
290C VAL* 3.8 28.5 - - + -
300C LEU* 3.9 30.7 - - + +
301C LEU* 1.3 70.2 - - - +
303C LEU* 1.3 62.4 + - - +
320C GLU 3.6 22.4 - - - +
324C ALA* 4.0 18.2 - - + -
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C SER* 3.4 22.9 - - - +
139C ASN* 3.5 18.8 - - + +
140C TRP* 3.6 5.9 - - - -
143C GLY* 3.8 12.6 - - - +
160C ASP* 4.0 6.3 - - - +
161C ILE* 3.6 33.7 - - + -
263C VAL* 3.8 24.0 - - + -
264C LEU 2.9 9.6 + - - +
265C GLN* 4.5 4.0 - - - -
266C CYS* 2.8 31.2 + - - +
301C LEU* 3.7 25.8 - - + -
302C MET* 1.3 82.7 - - - +
304C GLY* 1.3 62.7 + - - +
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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