Contacts of the helix formed by residues 339 - 352 (chain C) in PDB entry 3RMD
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 GLN 339 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335C ASP* 2.5 29.5 + - - -
336C ALA* 3.3 23.3 + - - +
337C LYS 3.7 11.4 - - - +
338C ARG* 1.3 77.0 - - - +
340C PHE* 1.3 61.8 + - - +
341C ILE 3.5 2.0 - - - -
342C ASN* 3.8 17.9 + - + +
343C LEU* 3.3 21.8 + - - +
550C VAL* 4.4 18.0 - - - +
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Residues in contact with PHE 340 (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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273C TYR* 3.3 28.4 + + + +
276C LEU* 3.8 19.5 - - + -
277C TYR* 4.1 28.0 - + - -
280C PHE* 3.4 47.3 - + + -
281C SER* 3.9 2.2 - - - -
335C ASP* 3.1 4.9 + - - -
338C ARG* 3.3 51.1 - - + -
339C GLN* 1.3 76.0 - - - +
341C ILE* 1.3 65.7 + - - +
342C ASN 3.2 2.0 - - - -
343C LEU* 3.3 15.7 + - + +
344C SER* 2.9 29.9 + - - -
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Residues in contact with ILE 341 (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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110C VAL* 4.4 27.6 - - + -
212C ILE* 4.4 17.0 - - + -
214C THR* 4.2 23.1 - - + +
271C LEU* 4.6 5.1 - - + +
273C TYR* 3.8 18.2 - - + -
276C LEU* 3.6 24.5 - - + -
335C ASP* 3.3 25.8 + - - +
340C PHE* 1.3 77.4 - - - +
342C ASN* 1.3 63.1 + - - +
344C SER* 3.4 4.1 + - - -
345C LEU* 3.2 30.1 + - + +
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Residues in contact with ASN 342 (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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103C TYR* 4.2 12.6 + - - -
105C HIS* 4.2 21.5 - - - +
335C ASP* 4.9 0.2 + - - -
339C GLN* 3.8 24.2 + - + +
340C PHE 3.2 0.4 - - - -
341C ILE* 1.3 78.4 - - - +
343C LEU* 1.3 66.4 + - - +
345C LEU* 3.0 20.6 + - - +
346C ASP* 2.9 22.7 + - - +
550C VAL* 5.0 6.5 - - - +
551C ALA* 6.0 1.4 - - - +
554C THR* 4.3 19.2 + - + +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C PHE* 3.9 23.3 - - + -
338C ARG 5.7 0.9 - - - +
339C GLN 3.3 15.5 + - - +
340C PHE* 3.7 24.2 - - + +
342C ASN* 1.3 79.3 - - - +
344C SER* 1.3 57.6 + - - +
346C ASP* 3.4 0.5 + - - +
347C MET* 3.0 43.8 + - + +
554C THR* 4.1 15.4 - - + +
557C ILE* 4.0 24.7 - - + -
558C ASN* 3.2 36.4 - - - +
561C LEU* 4.1 5.2 - - + -
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Residues in contact with SER 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.9 21.8 - - - -
276C LEU* 3.6 22.5 - - - +
280C PHE* 4.2 4.5 - - - -
340C PHE 2.9 17.9 + - - -
341C ILE 3.6 5.2 - - - -
342C ASN 3.1 0.2 - - - -
343C LEU* 1.3 78.3 - - - +
345C LEU* 1.3 60.6 + - - +
347C MET* 3.2 1.3 + - - -
348C GLY* 2.8 27.0 + - - -
355C ILE* 3.9 4.1 - - - +
358C VAL* 3.5 25.3 - - - +
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Residues in contact with LEU 345 (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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103C TYR* 3.7 20.2 - - + -
105C HIS* 4.4 6.7 - - + -
108C ILE* 3.9 31.6 - - + -
110C VAL* 5.4 4.3 - - + -
212C ILE* 4.0 32.1 - - + -
271C LEU* 6.1 0.4 - - + -
341C ILE* 3.2 22.4 + - + +
342C ASN* 3.0 20.0 + - - +
344C SER* 1.3 77.4 - - - +
346C ASP* 1.3 63.8 - - - +
348C GLY* 3.2 0.5 + - - -
349C TYR* 3.0 36.5 + - + +
355C ILE* 4.2 17.7 - - + -
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Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.3 28.0 + - - +
342C ASN 2.9 10.7 + - - +
343C LEU 3.6 7.6 - - - +
345C LEU* 1.3 78.4 - - - +
347C MET* 1.3 62.1 + - - +
349C TYR* 4.1 1.4 - - - +
350C TYR* 3.2 23.5 + - - +
551C ALA* 5.7 1.9 - - - +
554C THR* 3.7 20.1 - - + +
555C ALA* 3.5 30.7 + - - +
558C ASN* 3.9 6.7 - - - +
559C ARG* 4.7 6.0 + - - -
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Residues in contact with MET 347 (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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279C LYS* 5.5 0.4 - - - -
280C PHE* 3.9 20.2 - - + -
343C LEU* 3.0 36.9 + - + +
344C SER* 3.7 3.4 - - - +
346C ASP* 1.3 77.3 - - - +
348C GLY* 1.3 65.2 + - - +
350C TYR* 3.2 7.4 + - + +
351C ALA* 3.2 22.2 + - + +
353C ILE* 6.0 0.2 - - + -
358C VAL* 4.3 22.7 - - + +
364C THR* 4.5 15.7 - - + -
558C ASN* 3.1 19.9 + - - +
561C LEU* 4.3 9.4 - - + -
562C LEU* 3.7 33.7 - - + -
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Residues in contact with GLY 348 (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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5C TYR* 3.7 5.8 - - - -
344C SER 2.8 20.3 + - - -
347C MET* 1.3 75.1 - - - +
349C TYR* 1.3 50.9 + - - +
351C ALA* 3.2 0.7 + - - -
352C LYS 2.7 31.0 + - - -
353C ILE* 3.2 23.3 + - - +
355C ILE* 3.7 14.8 - - - -
358C VAL* 3.9 6.7 - - - +
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Residues in contact with TYR 349 (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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4C PHE* 3.8 13.7 - + - -
5C TYR* 2.7 66.9 + + - -
6C LEU* 4.1 9.0 + - - +
101C ILE* 3.8 38.1 + - + +
103C TYR* 3.3 44.9 - + + -
108C ILE* 3.7 19.4 - - + +
211C VAL* 5.8 0.2 - - - +
345C LEU* 3.0 33.9 + - + +
346C ASP 4.3 2.2 - - - +
348C GLY* 1.3 72.4 - - - +
350C TYR* 1.3 64.4 + - - +
351C ALA 3.3 0.2 - - - -
352C LYS* 3.6 15.0 + - - +
355C ILE* 4.1 9.5 - - + +
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Residues in contact with TYR 350 (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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346C ASP* 3.2 15.7 + - - +
347C MET* 3.4 12.3 - - + +
348C GLY 3.1 0.8 - - - -
349C TYR* 1.3 80.7 - - - +
351C ALA* 1.3 60.1 + - - +
352C LYS* 4.4 6.1 - - - +
368C ILE* 3.5 38.4 - - + +
477C LYS* 5.2 2.3 - - - -
478C VAL* 4.0 11.4 - - + +
481C GLN* 2.4 45.6 + - - -
558C ASN* 6.3 2.0 - - + -
559C ARG* 3.4 30.7 + - - +
562C LEU* 4.7 16.4 - - + -
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Residues in contact with ALA 351 (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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347C MET* 3.2 12.9 + - + +
348C GLY 3.8 1.3 - - - +
350C TYR* 1.3 79.7 - - - +
352C LYS* 1.3 71.3 + - - +
353C ILE* 3.8 23.8 - - + -
364C THR* 4.0 11.4 - - + +
367C ALA* 3.5 8.5 - - - +
368C ILE* 3.7 29.6 - - + +
371C ASN* 3.4 15.0 + - - -
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Residues in contact with LYS 352 (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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5C TYR* 3.4 11.9 - - + -
90C LEU* 4.2 10.2 - - - +
93C LEU* 3.5 26.3 - - + +
94C SER* 4.5 8.3 + - - +
97C TYR 2.7 29.9 + - - +
98C ASN* 4.1 4.2 - - - +
99C TYR* 3.0 28.6 + - - +
100C GLU* 5.3 0.7 - - - +
101C ILE* 4.1 15.9 - - + +
348C GLY 2.7 14.2 + - - -
349C TYR 3.6 13.0 + - - +
350C TYR 3.4 4.6 - - - +
351C ALA* 1.3 79.2 - - - +
353C ILE* 1.3 59.8 + - - +
367C ALA* 4.6 0.5 - - - +
371C ASN* 3.6 32.9 + - + +
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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