Contacts of the helix formed by residues 659 - 675 (chain D) in PDB entry 2P5G
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 MSE 659 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408D MSE 3.5 32.8 - - + -
410D PHE* 3.5 27.6 - - + -
601D VAL* 5.0 11.8 - - + +
604D TYR* 3.8 17.4 - - + -
605D LEU* 3.8 32.8 - - - -
627D VAL* 4.4 5.6 - - + -
632D ILE* 5.0 1.3 - - + -
654D PHE* 3.2 26.8 + - + +
655D ALA* 3.2 23.5 + - + +
658D ARG* 1.3 77.3 - - - +
660D GLU* 1.3 62.4 + - - +
661D PRO 3.3 0.2 - - - -
662D ALA* 2.9 20.4 + - - +
663D ILE* 3.0 12.6 + - - +
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Residues in contact with GLU 660 (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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410D PHE* 4.0 15.3 - - + -
655D ALA 2.7 20.0 + - - +
656D ARG* 4.0 9.6 - - + +
659D MSE 1.3 70.7 - - - +
661D PRO* 1.4 61.7 - - + +
663D ILE* 3.2 10.8 + - - +
664D ASP* 2.9 32.9 + - - +
667D PHE* 4.9 2.3 - - - -
682D PHE* 5.5 1.0 - - - +
683D MSE 3.4 53.6 + - - +
684D ASP* 4.8 1.1 - - - -
685D ARG* 5.0 1.7 + - + +
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Residues in contact with PRO 661 (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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656D ARG 3.3 19.1 - - - +
657D GLU 3.5 20.9 - - - +
658D ARG* 3.7 10.3 - - - +
659D MSE 3.4 3.4 - - - -
660D GLU* 1.4 90.9 - - + +
662D ALA* 1.3 55.8 + - - +
664D ASP* 3.5 10.3 - - + +
665D ARG* 3.0 27.5 + - - +
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Residues in contact with ALA 662 (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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597D ILE* 5.3 0.2 - - - +
600D LYS* 5.9 2.1 - - - +
601D VAL* 6.3 0.7 - - - -
604D TYR* 3.7 34.3 - - + -
658D ARG 3.5 13.5 - - - +
659D MSE 2.9 11.5 + - - +
661D PRO* 1.3 80.8 - - - +
663D ILE* 1.3 56.8 + - - +
665D ARG* 3.7 6.9 + - - +
666D GLY* 3.2 20.3 + - - -
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Residues in contact with ILE 663 (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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597D ILE* 3.7 18.5 - - + +
601D VAL* 5.1 6.0 - - + +
659D MSE 3.0 10.8 + - - +
660D GLU* 3.4 15.7 - - - +
662D ALA* 1.3 76.1 - - - +
664D ASP* 1.3 54.2 + - - +
666D GLY* 3.0 1.9 + - - -
667D PHE* 2.7 43.4 + - + -
683D MSE 3.7 30.5 - - + -
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Residues in contact with ASP 664 (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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660D GLU* 2.9 20.4 + - + +
661D PRO* 3.3 13.9 + - + +
663D ILE* 1.3 77.4 - - - +
665D ARG* 1.3 56.6 + - - +
667D PHE* 3.9 8.2 - - - +
668D ARG* 2.9 30.1 + - - +
679D HIS* 4.2 15.0 + - - -
682D PHE* 5.7 6.9 - - - +
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Residues in contact with ARG 665 (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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661D PRO 3.0 16.5 + - - +
662D ALA* 3.9 8.3 - - - +
663D ILE 3.3 0.2 - - - -
664D ASP* 1.3 76.1 - - - +
666D GLY* 1.3 56.1 + - - +
668D ARG* 4.0 6.0 - - - +
669D GLU* 3.1 27.9 + - - +
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Residues in contact with GLY 666 (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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596D TRP* 2.7 34.6 + - - -
597D ILE* 4.6 4.5 - - - -
600D LYS* 5.2 7.0 - - - -
662D ALA 3.2 11.9 + - - -
663D ILE* 3.0 9.2 + - - -
665D ARG* 1.3 77.3 - - - +
667D PHE* 1.3 61.7 + - - +
669D GLU* 3.9 4.4 + - - +
670D MSE 3.4 8.8 + - - -
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Residues in contact with PHE 667 (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* 3.9 23.6 - - + -
422D GLN* 5.5 1.6 + - - -
593D ALA* 4.5 7.2 - - + -
596D TRP* 4.9 0.9 - + - -
597D ILE* 3.7 35.9 - - + -
660D GLU* 4.9 1.8 - - - -
663D ILE* 2.7 32.3 + - + +
664D ASP* 3.9 6.3 - - - +
666D GLY* 1.3 72.8 - - - +
668D ARG* 1.3 51.7 + - - +
669D GLU 3.3 0.2 - - - -
670D MSE 3.0 32.6 + - + +
671D CYS* 2.8 32.2 + - - +
679D HIS* 3.0 25.2 + + + +
681D MSE 3.6 23.3 - - + +
682D PHE* 5.3 0.7 - - - -
683D MSE 3.7 30.1 - - + -
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Residues in contact with ARG 668 (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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664D ASP* 2.9 22.0 + - - +
665D ARG* 4.2 5.8 - - - +
667D PHE* 1.3 75.4 - - - +
669D GLU* 1.3 57.4 + - - +
670D MSE 3.1 0.2 - - - -
671D CYS* 3.0 18.3 + - - +
672D GLU* 3.1 15.6 + - - +
679D HIS* 3.6 17.2 + - + -
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Residues in contact with GLU 669 (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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596D TRP* 4.3 12.3 - - + -
665D ARG 3.1 21.3 + - - +
666D GLY* 4.0 8.1 - - - +
667D PHE 3.3 0.2 - - - -
668D ARG* 1.3 75.1 - - - +
670D MSE 1.3 56.7 + - - +
672D GLU* 4.3 6.5 - - - +
673D TYR* 3.3 20.1 + - - +
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Residues in contact with MSE 670 (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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422D GLN* 5.4 1.1 - - - +
589D PHE* 4.8 5.1 - - + -
592D MSE 3.7 31.4 - - + -
593D ALA* 3.8 16.8 - - + -
596D TRP* 3.6 38.1 - - + +
666D GLY 3.4 10.3 + - - +
667D PHE* 3.0 37.1 + - + +
669D GLU* 1.3 77.4 - - - +
671D CYS* 1.3 59.4 + - - +
672D GLU 3.4 0.7 - - - -
673D TYR* 3.7 7.2 - - + -
674D MSE 2.9 32.2 + - + +
676D ASN* 4.1 0.2 - - - +
681D MSE 3.4 33.7 - - + -
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Residues in contact with CYS 671 (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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422D GLN* 3.7 33.7 - - - +
667D PHE 2.8 11.2 + - - +
668D ARG* 3.0 14.5 + - - +
670D MSE 1.3 76.9 - - - +
672D GLU* 1.3 58.2 + - - +
675D ASN* 3.0 21.3 + - - -
676D ASN* 3.3 27.2 + - - -
678D GLN* 4.7 0.7 - - - -
679D HIS* 3.9 27.4 - - + -
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Residues in contact with GLU 672 (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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449D ARG* 3.5 28.4 + - - +
668D ARG 3.1 13.0 + - - +
669D GLU* 4.7 5.4 - - - +
671D CYS* 1.3 75.7 - - - +
673D TYR* 1.3 62.7 + - - +
674D MSE 3.4 0.2 - - - -
675D ASN* 3.6 4.7 + - - +
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Residues in contact with TYR 673 (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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442D TYR* 3.9 32.4 - + + -
445D ALA* 3.5 25.4 - - + -
447D ALA 2.7 32.5 + - - -
448D GLU 4.2 0.6 + - - -
449D ARG* 3.4 43.7 - - + +
450D PRO* 3.8 1.6 - - - +
592D MSE 5.5 1.3 - - - -
596D TRP* 4.1 17.5 - + - -
669D GLU 3.3 19.0 + - - +
670D MSE 3.6 9.1 - - + +
672D GLU* 1.3 81.0 - - - +
674D MSE 1.3 88.5 + - + +
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Residues in contact with MSE 674 (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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434D PHE* 6.1 0.2 - - - -
442D TYR* 3.8 13.2 - - + -
450D PRO* 3.6 27.1 - - + -
451D SER 5.1 0.4 - - - -
456D CYS* 3.0 53.9 + - - +
457D SER 4.8 0.2 - - - -
458D PRO* 4.4 10.3 - - - -
589D PHE* 3.8 7.0 - - + -
592D MSE 3.8 34.8 - - + +
670D MSE 2.9 18.4 + - + +
673D TYR* 1.3 120.9 - - + +
675D ASN* 1.3 65.5 + - - +
676D ASN* 3.1 17.9 - - - +
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Residues in contact with ASN 675 (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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449D ARG* 3.1 28.3 + - - +
451D SER 3.6 8.1 - - - +
452D ASP 2.9 27.3 + - - +
453D VAL 3.7 0.4 - - - -
454D TYR 2.9 26.0 + - - +
455D SER* 2.9 19.1 - - - -
465D LYS* 2.9 30.3 + - - +
671D CYS 3.0 13.6 + - - -
672D GLU* 3.6 4.5 + - - +
673D TYR 3.4 1.6 - - - -
674D MSE 1.3 78.6 - - - +
676D ASN* 1.3 59.3 + - - +
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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