Contacts of the strand formed by residues 373 - 377 (chain A) in PDB entry 3ELP
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 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PRO* 4.6 13.0 - - + +
163A THR* 5.0 8.7 - - - +
290A ILE* 5.6 0.2 - - + -
315A THR* 3.7 21.5 - - + -
316A PHE 3.7 3.8 - - - +
317A TYR* 3.7 28.7 - - + +
350A LEU* 3.1 21.0 - - - +
351A PRO* 3.7 29.5 - - + +
352A ALA 5.3 0.2 + - - -
369A ILE* 3.7 22.4 - - + -
370A SER* 3.0 20.9 + - - +
372A THR* 1.3 76.7 - - - +
374A ILE* 1.3 77.3 + - - +
375A ARG* 4.0 1.1 - - + +
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Residues in contact with ILE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL 3.8 0.9 - - - +
315A THR* 3.2 3.6 - - - +
316A PHE* 2.8 71.3 + - + +
318A ILE* 4.1 18.2 - - + -
325A ALA* 4.3 7.9 - - + +
328A PHE* 3.3 35.4 - - + -
329A LEU* 4.5 4.9 - - + -
349A GLU 3.2 16.8 - - - +
350A LEU* 4.0 13.2 - - + -
372A THR 4.4 2.0 - - - +
373A LEU* 1.3 85.8 - - - +
375A ARG* 1.3 63.6 + - - +
376A LEU* 4.0 16.6 - - + -
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASN* 3.4 29.9 + - - +
162A PRO* 3.6 18.8 - - + +
313A MET* 3.6 19.2 - - + +
314A VAL 3.6 2.9 - - - -
315A THR* 4.2 11.7 - - - +
339A GLU 3.2 24.9 + - - -
340A SER 3.8 6.7 + - - -
341A LEU* 3.6 34.7 - - - +
347A LEU 4.2 0.3 - - - +
348A ALA* 3.8 1.9 - - - -
349A GLU* 2.8 64.6 + - - +
351A PRO* 4.4 4.4 - - + +
373A LEU* 4.0 2.7 - - + +
374A ILE* 1.3 74.4 - - - +
376A LEU* 1.3 70.5 + - - +
377A SER* 4.7 8.3 - - - -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL* 3.7 29.6 - - + -
280A LEU* 4.1 15.0 - - + -
313A MET* 3.4 5.2 - - - +
314A VAL* 2.6 42.1 + - + +
316A PHE* 4.2 12.1 - - + -
328A PHE* 5.0 3.1 - - + -
335A PHE* 3.9 26.2 - - + -
347A LEU 3.3 2.0 - - - +
348A ALA* 3.9 26.9 - - + -
374A ILE* 4.0 14.4 - - + -
375A ARG* 1.3 82.8 + - - +
377A SER* 1.3 60.7 + - - +
378A VAL* 3.8 4.0 - - + -
390A LEU* 4.1 12.1 - - + -
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A HIS* 6.1 0.2 - - - -
312A GLY 3.7 4.6 - - - -
313A MET* 4.7 2.4 - - - +
340A SER 4.6 1.6 - - - -
341A LEU* 3.6 17.1 - - - +
342A GLY* 3.3 24.9 + - - -
345A GLU 3.8 2.6 + - - +
346A SER* 3.1 3.5 - - - -
347A LEU* 2.7 50.9 + - - +
375A ARG* 4.7 3.6 - - - -
376A LEU* 1.3 74.7 - - - +
378A VAL* 1.3 64.3 + - - +
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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