Contacts of the helix formed by residues 414 - 424 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412D LEU 3.2 5.4 + - - -
413D THR* 1.3 69.9 - - - +
415D LEU* 1.3 61.3 + - - +
416D TYR 3.6 1.6 - - - -
417D PRO* 3.0 7.6 - - - +
418D SER* 2.8 23.2 + - - -
479D PHE* 3.8 13.9 - - - -
482D ARG* 4.1 14.4 + - - -
563D ILE* 3.7 25.5 - - - +
564D ASN* 3.6 18.6 + - - -
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D LEU* 3.4 35.2 + - + -
413D THR 2.7 11.6 + - - +
414D SER* 1.3 69.0 - - - +
416D TYR* 1.3 67.2 + - + +
418D SER* 2.9 6.1 + - - -
419D ILE* 2.6 49.0 + - + +
590D GLY* 4.4 16.6 - - - +
593D ALA* 4.8 7.0 - - + -
622D THR* 2.9 33.2 - - - +
623D ASP* 4.4 6.3 - - + +
667D PHE* 6.5 0.4 - - + -
681D MET* 4.1 25.6 - - + -
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Residues in contact with TYR 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D GLY* 5.3 0.2 - - - -
394D ALA* 3.7 27.1 + - + +
415D LEU* 1.3 87.6 - - + +
417D PRO* 1.3 73.2 - - + +
419D ILE* 3.2 7.2 + - + +
420D ILE* 2.9 29.0 + - - +
567D TYR* 3.9 38.8 - + + -
586D ILE* 3.0 27.8 - - + +
587D THR* 3.5 44.1 + - + +
590D GLY* 5.0 7.2 - - - -
591D GLN 5.6 0.2 + - - -
622D THR* 4.0 13.8 + - - -
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Residues in contact with PRO 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D SER* 3.0 22.2 - - - +
416D TYR* 1.3 88.3 - - + +
418D SER* 1.3 61.2 + - - +
420D ILE* 3.2 14.8 + - + +
421D ARG* 3.0 29.1 + - - +
475D ILE* 3.9 17.3 - - + +
479D PHE* 4.1 4.7 - - + -
563D ILE* 3.0 48.5 - - + +
564D ASN* 4.6 4.9 - - - +
566D LEU* 5.2 2.7 - - + -
567D TYR* 5.3 4.7 - - + +
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Residues in contact with SER 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D THR* 2.8 18.3 + - - +
414D SER 2.8 16.0 + - - -
415D LEU 2.9 8.3 + - - -
417D PRO* 1.3 77.5 - - - +
419D ILE* 1.3 58.7 + - - +
421D ARG* 2.9 16.0 + - - +
422D GLN* 2.8 28.6 + - - +
479D PHE* 4.1 13.9 - - - -
680D LEU* 3.8 16.5 + - - +
681D MET* 3.7 18.6 - - - -
682D PHE* 5.6 0.9 - - - -
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Residues in contact with ILE 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D LEU* 2.6 30.5 + - + +
416D TYR* 3.7 11.7 - - + +
418D SER* 1.3 71.7 - - - +
420D ILE* 1.3 65.5 + - - +
422D GLN* 4.4 3.4 - - - -
423D VAL* 2.8 31.9 + - + +
425D ILE* 4.6 3.6 - - + -
586D ILE* 3.7 21.8 - - + +
589D PHE* 3.3 34.8 - - + -
590D GLY* 3.2 40.2 - - - +
681D MET* 3.8 18.4 - - + +
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Residues in contact with ILE 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416D TYR 2.9 21.4 + - - +
417D PRO* 3.3 11.0 - - + +
419D ILE* 1.3 76.9 - - - +
421D ARG* 1.3 58.0 + - - +
424D ASN* 2.8 24.8 + - - -
425D ILE* 3.1 37.9 + - + +
471D VAL* 3.9 11.0 - - + -
472D PRO* 3.7 14.7 - - + +
475D ILE* 4.6 3.6 - - + -
566D LEU* 4.1 20.2 - - + -
567D TYR* 5.0 7.9 - - + -
570D LEU* 3.4 27.8 - - + -
586D ILE* 3.6 21.1 - - + -
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Residues in contact with ARG 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D PRO 3.0 17.5 - - - +
418D SER* 2.9 11.8 + - - +
420D ILE* 1.3 73.8 - - - +
422D GLN* 1.3 64.7 + - - +
424D ASN* 3.2 16.1 + - - +
472D PRO* 4.5 9.1 - - - +
475D ILE* 3.9 16.6 - - + -
476D THR* 2.8 37.1 + - - +
479D PHE* 3.0 46.9 - - - +
480D ASN* 5.8 3.2 - - - +
677D LYS* 4.7 4.2 + - - +
678D GLN* 4.2 23.1 + - - +
680D LEU* 3.3 40.5 - - + +
682D PHE* 5.8 1.6 - - - -
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Residues in contact with GLN 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D SER 2.8 18.1 + - - +
419D ILE* 3.9 5.8 - - - +
421D ARG* 1.3 75.4 - - - +
423D VAL* 1.3 61.3 + - + +
589D PHE* 3.2 17.8 - - - -
670D MET* 4.3 4.6 - - - +
671D CYS* 4.3 8.2 - - - +
676D ASN* 2.9 31.8 + - + +
677D LYS* 3.0 27.5 + - - +
678D GLN* 2.9 24.4 + - - +
679D HIS* 3.3 7.3 - - - -
680D LEU* 2.7 36.2 + - + +
681D MET* 3.5 25.1 - - + +
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Residues in contact with VAL 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D ILE* 2.8 24.9 + - + +
422D GLN* 1.3 74.0 - - + +
424D ASN* 1.3 71.5 + - - +
425D ILE* 3.7 24.9 - - + -
455D SER* 2.9 30.5 + - - +
456D CYS 3.7 14.1 - - - +
457D SER* 4.8 1.3 - - - -
463D TYR* 3.9 18.9 - - + +
589D PHE* 3.2 44.0 - - + -
676D ASN* 4.1 3.1 - - - +
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Residues in contact with ASN 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D ILE 2.8 14.7 + - - -
421D ARG 3.2 10.0 + - - +
423D VAL* 1.3 84.2 - - - +
425D ILE* 1.3 58.7 + - - +
429D THR* 2.8 31.0 + - - +
463D TYR* 3.5 6.1 - - - +
464D TYR 2.9 25.2 - - - +
467D ARG 3.4 11.0 - - - +
468D ASP* 3.8 7.7 - - - +
469D GLY 3.3 23.1 - - - +
472D PRO* 3.8 13.4 - - - +
677D LYS* 4.0 26.3 - - + +
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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