Contacts of the strand formed by residues 333 - 337 (chain C) in PDB entry 5AQP
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 ASP 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.8 31.0 - - + +
188C LYS* 3.0 24.1 + - - -
193C ARG* 2.8 29.5 + - - -
194C ASN 3.3 2.6 + - - -
195C VAL* 3.4 16.2 - - + +
196C LEU 2.8 31.5 + - - +
331C ILE* 3.3 5.2 - - - +
332C HIS* 1.3 85.8 - - - +
334C ILE* 1.3 60.2 + - - +
335C VAL 4.2 0.4 - - - -
357C LYS* 4.4 1.8 - - - +
360C ASN* 4.0 9.5 + - - +
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Residues in contact with ILE 334 (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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196C LEU* 3.3 18.8 - - + +
331C ILE* 4.2 10.8 - - + -
333C ASP* 1.3 75.6 - - - +
335C VAL* 1.3 68.6 + - - +
336C LEU* 4.9 0.7 - - + -
350C LEU* 3.8 30.1 - - + -
354C PHE* 3.7 34.8 - - + -
357C LYS* 3.7 35.1 - - + +
358C GLU 4.4 3.3 + - - +
359C LEU* 3.8 22.9 - - + -
360C ASN* 2.9 33.3 + - - +
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.1 22.9 - - + +
183C TYR* 3.6 31.6 - - + -
185C LEU* 3.7 30.3 - - + -
195C VAL* 4.3 2.9 - - + -
196C LEU 2.8 9.9 + - - -
197C ILE* 3.6 23.2 - - + +
198C PHE* 2.8 33.4 + - - +
334C ILE* 1.3 77.2 - - - +
336C LEU* 1.4 67.5 + - - +
337C VAL* 4.0 2.4 + - + -
360C ASN* 3.8 11.7 - - + +
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Residues in contact with LEU 336 (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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183C TYR* 4.6 6.2 + - - -
198C PHE* 3.6 19.1 - - + -
334C ILE* 4.9 1.6 - - + -
335C VAL* 1.4 74.5 - - - +
337C VAL* 1.3 66.5 + - - +
341C THR* 3.7 23.1 - - - +
346C ILE* 5.9 1.1 - - + -
347C GLN* 3.8 31.9 - - + +
350C LEU* 3.5 31.6 - - + -
359C LEU* 3.9 19.5 - - + -
360C ASN 3.1 17.9 + - - +
361C LYS* 3.9 24.3 - - + -
363C ILE 5.1 0.9 - - - +
365C PRO* 4.4 8.4 - - + +
368C ALA* 5.1 0.3 - - - +
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Residues in contact with VAL 337 (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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175C GLU 6.5 0.2 - - - -
179C ALA* 3.7 21.8 - - + -
197C ILE* 3.8 19.1 - - + -
198C PHE 3.0 8.4 + - - +
199C ASP* 3.3 36.3 - - + +
200C LEU 3.0 22.3 + - - -
335C VAL* 4.2 4.9 - - + -
336C LEU* 1.3 79.1 - - - +
338C GLY* 1.3 61.9 + - - +
341C THR* 3.1 8.0 - - - +
365C PRO* 3.9 7.9 - - - +
368C ALA* 3.6 28.7 - - + -
369C VAL* 4.6 10.8 - - + -
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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