Contacts of the strand formed by residues 391 - 398 (chain C) in PDB entry 1EQR
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 MET 391 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C ARG* 3.4 1.6 - - - -
323C VAL* 2.8 49.0 + - + +
326C GLY 3.4 35.2 - - - +
329C LEU* 4.3 3.6 - - + -
334C ILE* 3.6 34.1 - - + -
351C TYR* 4.0 17.5 - - + -
352C ILE 3.6 24.0 - - - +
353C LYS* 3.7 23.3 - - + -
390C ASP* 1.3 74.1 - - - +
392C ILE* 1.3 64.5 + - - +
393C PHE* 3.7 28.7 - - + -
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Residues in contact with ILE 392 (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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320C ALA* 3.9 20.2 - - + -
321C LEU 3.4 4.5 - - - +
322C ARG* 4.0 15.9 - - + -
351C TYR* 3.2 6.2 - - - +
352C ILE* 2.9 44.9 + - + +
354C VAL* 3.9 18.6 - - + -
380C ILE* 4.1 6.5 - - + -
381C LEU* 4.0 9.0 - - + -
384C THR* 3.4 23.8 - - + +
386C ALA* 3.6 19.1 - - + -
391C MET* 1.3 79.0 - - - +
393C PHE* 1.3 62.3 + - - +
394C PHE* 3.8 22.8 - - + -
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Residues in contact with PHE 393 (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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319C ALA 3.5 0.7 - - - +
320C ALA* 3.2 5.9 - - - -
321C LEU* 2.7 41.0 + - + +
323C VAL* 3.6 26.9 - - + -
329C LEU* 4.0 24.9 - - + -
334C ILE* 4.3 14.6 - - + -
337C TYR* 4.2 13.9 - + - -
349C LEU* 3.4 31.4 - - + -
350C ALA 3.5 0.9 - - - -
351C TYR* 3.7 25.6 - - + -
391C MET* 3.7 23.1 - - + -
392C ILE* 1.3 73.0 - - - +
394C PHE* 1.3 61.0 + - - +
406C MET* 4.0 17.2 - - + +
409C LEU* 4.2 12.1 - - + -
413C VAL* 4.7 6.3 - - + -
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Residues in contact with PHE 394 (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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295C VAL* 4.2 12.3 - - + -
299C LEU* 5.4 1.3 - - + -
307C PHE* 4.1 23.3 - + + -
318C VAL* 4.5 8.1 - - + -
319C ALA 3.2 6.1 - - - -
320C ALA* 3.8 22.9 - - + -
348C GLY 4.4 1.6 - - - +
349C LEU* 3.7 12.7 - - - +
350C ALA* 2.8 54.8 + - + +
351C TYR 4.2 0.4 - - - -
352C ILE* 3.3 42.8 - - + -
368C VAL* 5.0 1.6 - - + -
372C LEU* 5.5 0.4 - - + -
380C ILE* 3.9 23.1 - - + -
392C ILE* 3.8 20.4 - - + -
393C PHE* 1.3 78.0 - - - +
395C GLY* 1.3 60.4 + - - +
396C ALA* 4.1 0.9 + - - -
406C MET* 4.3 4.5 - - - -
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Residues in contact with GLY 395 (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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317C ARG 3.3 2.9 - - - +
318C VAL* 3.3 2.1 - - - -
319C ALA* 2.7 41.2 + - - -
348C GLY 5.5 2.7 - - - -
349C LEU* 5.3 0.2 - - - -
394C PHE* 1.3 73.4 - - - +
396C ALA* 1.3 59.8 + - - -
402C VAL* 3.5 10.9 - - - +
405C ALA* 6.4 0.4 - - - -
406C MET* 3.8 25.0 - - - -
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Residues in contact with ALA 396 (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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306C VAL* 3.5 29.0 - - + +
307C PHE* 4.0 22.4 - - + -
310C PRO* 3.8 13.5 - - + +
317C ARG 3.6 5.6 - - - -
318C VAL* 4.2 5.4 - - + -
347C LYS* 6.0 0.3 - - - +
348C GLY 5.9 0.4 + - - -
394C PHE 4.1 1.6 + - - -
395C GLY* 1.3 73.5 - - - +
397C ASP* 1.3 67.7 + - - +
402C VAL* 4.1 0.2 - - - +
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Residues in contact with ASP 397 (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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310C PRO* 3.8 11.8 - - - +
313C ASP* 5.7 0.4 - - - -
316C GLY* 3.2 2.8 - - - -
317C ARG 3.0 26.4 + - - +
345C GLY 4.0 12.5 - - - +
346C ALA* 4.5 0.6 - - - -
347C LYS* 4.1 27.6 + - - +
396C ALA* 1.3 76.0 - - - +
398C ASN* 1.3 74.5 + - - +
401C ILE* 3.9 36.8 - - + +
402C VAL* 3.3 12.3 - - + +
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Residues in contact with ASN 398 (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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313C ASP* 5.1 4.0 - - - +
315C LYS* 3.3 16.6 - - + +
316C GLY* 3.7 2.0 - - - -
397C ASP* 1.3 83.8 + - - +
399C LYS* 1.3 64.4 + - - +
400C LYS* 3.1 9.5 + - - +
401C ILE* 2.7 47.3 + - - +
402C VAL* 3.1 8.2 + - - -
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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