Contacts of the strand formed by residues 304 - 308 (chain E) in PDB entry 5IJ7
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 304 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A MET* 4.2 10.8 - - + -
42A PHE* 4.1 28.5 - - + -
45A ASN* 3.8 28.9 - - + +
300E TRP* 3.5 7.3 - - - -
301E LEU* 2.9 32.2 + - + +
303E ASP* 1.4 81.7 - - + +
305E ILE* 1.3 64.9 + - - +
316E CYS* 4.1 11.2 - - - -
317E TRP 3.7 5.8 - - - +
318E LYS* 4.0 26.7 - - + -
339E LEU* 3.8 33.2 - - + -
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E MET* 3.7 29.6 - - + -
298E VAL* 3.6 30.3 - - + -
299E ARG 3.9 3.4 - - - +
300E TRP* 3.8 20.9 - - + -
303E ASP 4.1 1.3 - - - +
304E LEU* 1.3 79.5 - - - +
306E LEU* 1.3 66.9 + - - +
307E SER* 4.5 0.2 - - - -
315E VAL 3.4 1.4 - - - +
316E CYS* 3.3 6.5 - - - -
317E TRP* 2.8 69.1 + - + +
319E PRO* 3.7 30.3 - - + -
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Residues in contact with LEU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E VAL* 3.4 1.6 - - - +
299E ARG 2.8 39.3 + - - +
301E LEU* 3.9 33.0 - - + -
305E ILE* 1.3 71.4 - - - +
307E SER* 1.4 61.8 + - - +
314E ILE* 3.9 11.4 - - + -
315E VAL 3.4 1.3 - - - -
316E CYS* 3.8 28.5 - - + -
342E PHE* 3.8 20.0 - - + -
354E PHE* 3.2 21.6 - - + -
356E MET* 3.9 26.5 - - + -
363E LEU* 4.8 8.7 - - + -
377E LEU* 4.5 6.1 - - + -
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Residues in contact with SER 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E LEU* 3.7 23.0 - - - +
291E HIS* 2.9 32.1 + - - -
295E VAL* 3.9 1.6 - - - -
297E CYS 3.3 13.9 - - - -
298E VAL* 4.2 1.6 - - - -
306E LEU* 1.4 74.6 - - - +
308E LYS* 1.3 61.7 + - - +
314E ILE* 3.5 2.5 - - - +
315E VAL 2.8 35.0 + - - -
317E TRP* 3.1 21.0 + - - -
354E PHE* 4.0 4.9 - - - -
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Residues in contact with LYS 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E HIS* 3.6 7.2 - - - -
295E VAL* 3.1 21.0 - - - +
296E ASP* 2.8 46.9 + - - +
297E CYS* 3.2 7.9 + - + +
307E SER* 1.3 77.0 - - - +
309E SER* 1.3 71.4 + - - +
310E CYS* 5.7 0.2 - - - +
313E ALA 3.5 15.5 - - - +
314E ILE* 4.0 6.5 - - + -
344E TYR* 3.4 19.3 - - - +
347E CYS* 4.1 17.9 + - - -
349E ILE 5.2 1.4 + - - -
352E MET* 2.8 30.7 + - - +
354E PHE* 3.7 26.9 - - + -
365E LEU* 4.1 12.3 - - + -
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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