Contacts of the helix formed by residues 666 - 680 (chain B) in PDB entry 5N4D
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 PRO 666 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ARG* 6.3 0.7 - - - +
657B VAL* 3.5 32.1 - - + -
658B ASN 5.6 0.7 - - - +
659B ILE* 3.5 22.4 - - + -
664B VAL 3.3 5.1 - - - +
665B VAL* 1.3 84.2 - - + +
667B MET* 1.4 65.2 + - - +
668B HIS 3.0 4.0 + - - -
669B SER* 3.0 7.8 + - - +
670B PHE* 2.9 44.3 + - + -
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Residues in contact with MET 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU 3.5 24.0 - - - +
41B GLU* 3.1 30.1 - - + +
606B ASP* 4.4 7.0 - - - +
609B LYS* 5.7 0.9 - - - -
613B PHE* 4.5 16.8 - - + -
665B VAL* 3.2 19.9 - - + -
666B PRO* 1.4 81.4 - - - +
668B HIS* 1.3 82.5 + - - +
670B PHE* 3.7 5.7 - - - -
671B LYS* 2.9 75.5 + - + +
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Residues in contact with HIS 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLY 3.2 17.7 - - - +
604B VAL* 3.6 18.4 - - + +
605B ALA* 3.1 17.2 + - - +
606B ASP* 3.1 48.9 + - + +
609B LYS 5.1 0.4 - - - -
610B PHE* 3.7 21.2 + - + +
613B PHE* 5.5 1.2 - - - -
619B TRP* 4.9 2.6 - - - -
641B VAL* 4.3 0.5 - - - +
664B VAL* 3.4 15.0 - - + +
665B VAL* 3.2 37.8 - - + +
666B PRO 3.0 0.6 - - - -
667B MET* 1.3 87.3 - - - +
669B SER* 1.3 62.6 + - - +
671B LYS* 3.5 2.8 + - - +
672B PHE* 3.0 24.1 + - - +
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Residues in contact with SER 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET* 4.4 5.9 - - - +
602B GLY* 4.4 2.6 - - - -
603B GLY 4.0 20.6 + - - -
655B ILE* 3.7 20.6 - - - +
657B VAL* 3.5 33.3 - - - +
666B PRO* 3.0 6.3 + - - +
668B HIS* 1.3 78.3 - - - +
670B PHE* 1.4 64.8 + - - +
672B PHE* 3.3 5.8 + - - +
673B ILE* 3.0 26.7 + - - +
689B ILE* 4.0 2.0 - - - +
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Residues in contact with PHE 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.7 36.6 - - + -
42B GLU 5.9 0.4 - - - -
47B VAL* 4.4 9.4 - - + -
50B TRP* 3.7 29.4 - + + -
51B THR* 3.7 22.2 - - + -
657B VAL* 4.5 4.0 - - + -
659B ILE* 5.0 1.8 - - + -
666B PRO* 2.9 48.3 + - + +
667B MET* 3.8 4.9 - - - +
669B SER* 1.4 76.8 - - - +
671B LYS* 1.3 57.2 + - - +
673B ILE* 3.3 4.1 - - - +
674B ALA* 3.0 31.0 + - - +
689B ILE* 3.9 11.4 - - + -
691B ILE* 3.9 30.7 - - + -
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Residues in contact with LYS 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 2.7 38.2 + - - +
37B TYR* 3.5 37.0 - - + +
38B GLN* 3.9 0.4 - - - +
40B LEU* 4.6 2.2 - - + -
41B GLU* 2.7 19.6 + - - -
606B ASP* 2.9 30.2 + - + +
609B LYS* 3.9 1.4 - - - +
641B VAL* 4.1 16.6 - - + -
667B MET* 2.9 40.3 + - + +
668B HIS 3.9 2.5 - - - +
670B PHE* 1.3 75.1 - - - +
672B PHE* 1.3 58.7 + - - +
674B ALA* 3.4 5.6 + - - +
675B THR* 2.7 36.0 + - - +
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Residues in contact with PHE 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET* 3.4 56.8 - - + -
587B ILE* 4.3 10.1 - - + -
588B VAL* 3.9 10.5 - - + -
605B ALA* 4.0 3.4 - - + -
640B PRO* 3.6 43.3 - - + -
641B VAL* 4.0 8.5 - - + +
644B VAL* 3.8 12.6 - - + -
653B THR* 5.6 0.7 - - + -
655B ILE* 3.7 14.4 - - + -
668B HIS 3.0 17.8 + - - +
669B SER 3.8 3.4 - - - +
670B PHE 3.2 0.2 - - - -
671B LYS* 1.3 77.4 - - - +
673B ILE* 1.3 57.5 + - - +
675B THR* 3.2 3.4 + - - -
676B LEU* 2.8 53.2 + - + +
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Residues in contact with ILE 673 (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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50B TRP* 3.7 21.5 - - + -
54B GLN* 5.1 0.4 - - - -
653B THR* 5.4 0.7 - - + -
655B ILE* 3.9 18.8 - - + +
669B SER 3.0 17.1 + - - +
670B PHE 3.3 10.8 - - - +
672B PHE* 1.3 76.9 - - - +
674B ALA* 1.3 59.8 + - - +
676B LEU* 3.7 8.4 - - + +
677B GLN* 2.9 45.5 + - - +
687B LEU* 3.6 39.0 - - + +
688B LEU 3.7 10.5 - - - +
689B ILE* 3.9 26.0 - - + -
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Residues in contact with ALA 674 (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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14B THR* 3.9 18.8 - - + -
37B TYR* 3.7 33.2 + - + -
40B LEU* 4.0 4.9 - - + -
50B TRP* 4.3 5.6 - - + -
670B PHE 3.0 18.1 + - - +
671B LYS 3.7 3.4 - - - +
673B ILE* 1.3 78.9 - - - +
675B THR* 1.3 57.7 + - - +
677B GLN* 3.5 6.9 + - - +
678B HIS* 3.0 30.1 + - - +
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Residues in contact with THR 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 3.6 20.8 - - + -
641B VAL* 3.7 31.5 - - - +
644B VAL* 3.8 22.2 - - + -
671B LYS 2.7 22.2 + - - -
672B PHE* 3.7 5.6 - - - -
674B ALA* 1.3 74.3 - - - +
676B LEU* 1.4 64.9 + - - +
678B HIS* 3.2 1.9 + - - -
679B ASN* 2.9 42.7 + - - +
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Residues in contact with LEU 676 (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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587B ILE* 4.6 6.3 - - + -
588B VAL* 5.5 0.4 - - + -
644B VAL* 3.9 23.3 - - + -
650B MET* 4.0 29.8 - - + -
653B THR* 4.6 6.7 - - + -
672B PHE* 2.8 54.0 + - + +
673B ILE* 3.3 23.3 + - + +
675B THR* 1.4 77.7 - - - +
677B GLN* 1.3 63.4 + - - +
680B VAL* 3.0 32.2 + - + +
687B LEU* 4.0 22.8 - - + +
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Residues in contact with GLN 677 (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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11B TYR* 3.3 49.7 - - + +
12B PRO 4.4 3.5 - - - +
14B THR* 4.6 4.0 + - - -
54B GLN* 3.0 42.5 + - - -
57B LEU* 5.1 0.6 - - - +
673B ILE* 2.9 31.9 + - + +
674B ALA* 4.1 4.0 - - - +
676B LEU* 1.3 76.4 - - - +
678B HIS* 1.3 57.5 + - - +
681B PRO* 3.3 27.5 - - - +
687B LEU* 2.9 29.8 + - + +
688B LEU* 4.7 0.8 - - - +
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Residues in contact with HIS 678 (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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16B ARG* 3.3 45.9 + - - +
37B TYR* 3.2 23.1 - - + +
674B ALA 3.0 11.3 + - - +
675B THR* 3.8 3.8 - - - +
677B GLN* 1.3 78.3 - - - +
679B ASN* 1.3 82.6 + - - +
680B VAL 3.6 0.2 - - - -
681B PRO* 3.4 12.6 - - - +
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Residues in contact with ASN 679 (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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644B VAL* 3.1 43.6 + - + +
645B ARG 3.9 2.7 - - - +
646B THR* 3.4 37.8 - - + +
675B THR* 2.9 25.8 + - - +
678B HIS* 1.3 106.3 + - - +
680B VAL* 1.3 65.2 + - - +
681B PRO* 3.3 5.0 - - - +
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Residues in contact with VAL 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TYR* 4.9 0.9 - - - -
644B VAL* 5.4 0.7 - - + -
645B ARG 3.7 12.1 - - - +
646B THR 3.6 17.5 - - - +
648B LYS 3.7 21.3 - - - +
650B MET* 4.2 12.8 - - + -
676B LEU* 3.0 21.3 + - + +
679B ASN* 1.3 82.0 - - + +
681B PRO* 1.3 66.9 - - - +
682B GLN 3.2 2.7 - - - -
683B ASN* 2.9 30.7 + - + +
687B LEU* 3.7 20.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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