Contacts of the strand formed by residues 331 - 334 (chain C) in PDB entry 3EQL
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 ARG 331 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ILE* 3.4 41.9 - - + +
141C HIS* 2.9 18.9 - - - +
142C ARG* 4.7 2.2 - - + +
325C ILE* 4.2 13.7 - - + +
326C ASP* 4.3 29.3 + - - +
327C HIS 3.0 10.8 + - - +
328C LEU* 3.0 30.1 - - + +
330C ASN* 1.3 74.8 - - - +
332C ARG* 1.3 62.2 + - - +
333C ILE* 3.8 11.3 - - - +
412C ALA* 5.7 0.4 - - - +
427C VAL* 3.4 45.1 + - - +
434C HIS* 3.7 29.0 + - - -
450C GLY 5.6 2.2 + - - -
451C LEU* 5.7 1.2 + - - +
465C GLY 4.6 0.2 - - - +
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Residues in contact with ARG 332 (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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140C ILE* 3.0 27.5 - - - +
141C HIS* 2.7 42.3 + - + +
143C SER* 3.9 22.4 - - - +
144C PRO* 4.3 16.6 - - - +
165C LEU* 5.7 1.2 - - - +
265C ARG* 5.8 6.3 - - - +
267C TYR* 6.2 1.6 - - - -
330C ASN 3.5 1.4 + - - -
331C ARG* 1.3 72.1 - - - +
333C ILE* 1.3 69.6 + - - +
334C ARG* 4.5 0.2 - - - +
338C GLU* 3.0 42.3 + - - +
464C LEU* 3.3 45.3 - - - +
465C GLY 3.1 15.9 - - - +
466C PHE* 3.9 8.1 - - + -
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Residues in contact with ILE 333 (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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21C ILE* 5.8 2.0 - - + -
138C SER* 4.2 11.0 - - - -
139C GLN 3.1 7.4 - - - +
140C ILE* 3.8 16.2 - - + -
328C LEU* 4.8 3.8 - - + -
331C ARG 3.8 11.2 - - - +
332C ARG* 1.3 82.2 + - - +
334C ARG* 1.3 67.2 + - - +
335C THR* 3.5 6.5 + - + +
338C GLU* 4.2 2.3 - - - +
410C ILE* 4.1 22.7 - - + -
455C LEU* 6.1 1.8 - - + -
461C VAL* 4.3 17.3 - - + -
464C LEU* 5.4 0.2 - - - +
465C GLY* 2.8 37.0 + - - +
467C ILE* 3.2 46.2 - - + +
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Residues in contact with ARG 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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138C SER* 3.2 27.1 - - - -
139C GLN* 2.8 32.9 + - + +
141C HIS* 3.3 30.4 - - + +
165C LEU* 4.2 10.9 - - - +
332C ARG* 4.5 0.4 - - - +
333C ILE* 1.3 72.5 - - - +
335C THR* 1.3 62.6 + - - +
338C GLU* 3.2 36.8 + - - +
339C LEU* 3.3 19.5 - - + +
342C ASP* 4.8 10.6 + - - -
415C PRO* 3.1 33.3 - - - +
418C LEU* 3.2 32.6 - - - +
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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