Contacts of the helix formed by residues 414 - 424 (chain B) 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 SER 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B LEU 3.4 4.0 + - - -
413B THR* 1.3 81.3 + - - +
415B LEU* 1.3 61.4 + - - +
416B TYR 3.6 1.6 - - - -
417B PRO* 3.1 15.2 - - - +
418B SER* 2.5 28.4 + - - -
479B PHE* 3.1 30.1 - - - -
563B ILE* 4.6 5.8 - - - -
564B ASN* 5.6 0.4 - - - -
623B ASP* 5.5 0.2 + - - -
907B DTP 3.2 39.7 + - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B LEU* 4.1 23.3 + - + -
413B THR 2.9 9.3 + - - -
414B SER* 1.3 69.6 - - - +
416B TYR* 1.3 64.2 + - + +
418B SER* 2.9 5.9 + - - -
419B ILE* 2.6 68.0 + - + +
590B GLY* 4.4 16.6 - - - +
593B ALA* 4.8 1.6 - - + -
622B THR* 3.1 30.7 - - + +
623B ASP* 3.8 18.8 + - + -
681B MET* 4.0 20.9 - - + -
907B DTP 3.4 10.5 + - - +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ALA* 3.8 25.8 + - - +
415B LEU* 1.3 85.0 - - + +
417B PRO* 1.3 73.8 - - + +
419B ILE* 3.2 13.8 + - + +
420B ILE* 2.9 30.9 + - + +
567B TYR* 4.2 36.3 - + + -
586B ILE* 3.3 24.1 - - + +
587B THR* 3.6 41.6 + - + +
590B GLY* 5.0 1.8 - - - -
622B THR* 4.3 7.4 - - + +
907B DTP 3.0 42.2 + + + -
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Residues in contact with PRO 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B SER* 3.1 18.2 - - - +
416B TYR* 1.3 94.7 - - + +
418B SER* 1.3 60.4 + - - +
420B ILE* 3.2 16.6 - - + +
421B ARG* 3.1 27.3 + - - +
475B ILE* 4.1 17.6 - - + +
479B PHE* 4.0 19.5 - - + -
563B ILE* 3.8 31.0 - - + +
564B ASN* 5.8 0.2 - - - +
566B LEU* 5.8 3.1 - - + -
567B TYR* 6.0 3.6 - - + +
907B DTP 4.1 6.5 - - - +
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Residues in contact with SER 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B THR* 2.7 17.6 + - - +
414B SER* 2.5 28.3 + - - -
415B LEU 3.2 4.5 - - - -
417B PRO* 1.3 75.0 - - - +
419B ILE* 1.3 55.5 + - - +
421B ARG* 2.9 15.5 + - - +
422B GLN* 2.8 34.3 + - - +
479B PHE* 4.7 5.4 - - - -
680B LEU* 3.9 26.0 + - - +
681B MET* 4.0 9.0 - - - -
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 2.6 52.8 + - + +
416B TYR* 3.6 13.7 - - + +
418B SER* 1.3 70.5 - - - +
420B ILE* 1.3 64.0 + - - +
422B GLN* 4.5 2.9 - - - +
423B VAL* 2.8 32.5 + - + +
425B ILE* 4.6 2.2 - - + -
586B ILE* 3.7 20.6 - - + +
589B PHE* 3.5 35.4 - - + -
590B GLY* 3.4 28.9 - - - +
681B MET* 4.0 8.7 - - + -
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 2.9 27.8 + - + +
417B PRO* 3.2 16.4 - - + +
419B ILE* 1.3 76.2 - - - +
421B ARG* 1.3 54.7 + - - +
424B ASN* 2.8 29.1 + - - -
425B ILE* 3.0 36.1 + - + +
471B VAL* 4.3 7.0 - - + -
472B PRO* 3.9 20.3 - - + +
475B ILE* 4.6 4.5 - - + -
566B LEU* 4.5 11.7 - - + -
567B TYR* 5.7 3.8 - - + +
570B LEU* 3.5 30.7 - - + -
586B ILE* 3.8 22.0 - - + -
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B PRO 3.1 12.0 + - - +
418B SER* 2.9 8.8 + - - +
420B ILE* 1.3 80.6 - - - +
422B GLN* 1.3 62.7 + - - +
424B ASN* 3.2 15.9 + - - +
472B PRO* 4.3 13.3 - - + +
475B ILE* 4.0 15.9 - - - -
476B THR* 3.5 40.5 + - - +
479B PHE* 3.7 35.4 - - - -
677B LYS* 4.7 6.6 - - - +
678B GLN* 4.3 17.6 + - - +
680B LEU* 3.1 49.7 - - + +
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Residues in contact with GLN 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B SER 2.8 17.7 + - - +
419B ILE* 3.9 6.3 - - - +
421B ARG* 1.3 73.2 - - - +
423B VAL* 1.3 60.7 + - + +
589B PHE* 3.2 19.3 - - + -
670B MET* 4.4 1.2 - - - +
671B CYS* 4.1 15.5 - - - +
676B ASN* 2.9 29.6 + - + +
677B LYS* 3.0 28.9 + - - +
678B GLN 2.8 24.8 + - - +
679B HIS* 3.1 8.0 + - - -
680B LEU* 2.5 36.5 + - + +
681B MET* 3.5 22.8 + - + +
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 2.8 30.1 + - + +
422B GLN* 1.3 71.7 - - + +
424B ASN* 1.3 69.4 + - - +
425B ILE* 3.2 26.0 - - + -
455B SER* 2.9 28.4 + - - +
456B CYS 4.0 9.6 - - - +
457B SER* 4.7 1.8 - - - +
463B TYR* 3.3 24.8 - - + +
589B PHE* 3.6 40.2 - - + -
676B ASN* 4.0 3.8 - - - +
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Residues in contact with ASN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ILE 2.8 12.0 + - - -
421B ARG 3.2 5.6 + - - +
423B VAL* 1.3 84.4 - - - +
425B ILE* 1.3 61.1 + - - +
429B THR* 3.0 25.4 + - - +
463B TYR* 3.6 6.1 - - - +
464B TYR 2.6 28.7 + - - +
467B ARG 3.3 16.0 + - - -
468B ASP* 3.9 4.5 - - - +
469B GLY 3.3 22.7 + - - +
472B PRO* 3.6 12.1 - - - +
677B LYS* 3.6 31.1 - - + +
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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