Contacts of the helix formed by residues 669 - 681 (chain A) in PDB entry 4N78
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 ASP 669 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A LYS* 2.8 30.6 + - + +
665A LEU 3.1 12.2 + - - +
666A TYR* 3.4 17.0 - - + +
667A SER 3.2 0.6 - - - -
668A LEU* 1.3 73.4 - - - +
670A LEU* 1.3 62.7 + - - +
671A TYR 3.0 2.9 - - - -
672A ASN* 2.6 54.4 + - - +
673A ASP* 3.5 6.2 + - - +
756A GLN 4.4 1.6 - - - +
757A LEU* 5.0 1.6 - - - -
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Residues in contact with LEU 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ILE* 3.8 23.1 - - + -
459A LYS* 4.1 4.9 - - - -
618A LEU* 3.7 46.2 - - + +
621A LEU* 4.0 18.2 - - + -
645A PRO* 4.3 27.6 - - + -
648A LEU* 4.3 6.3 - - + -
666A TYR 3.8 4.2 + - - +
667A SER* 3.3 25.4 - - - +
668A LEU 3.0 0.6 - - - -
669A ASP* 1.3 78.6 - - - +
671A TYR* 1.3 62.3 + - - +
673A ASP* 3.3 14.2 + - - +
674A SER* 3.1 26.3 + - - +
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Residues in contact with TYR 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A TRP* 3.9 11.9 - + + -
645A PRO* 3.4 25.7 - - + +
646A TRP* 3.5 24.0 + + - +
649A THR* 5.4 0.2 - - - -
668A LEU* 3.3 43.4 + - + +
669A ASP 3.0 0.8 - - - -
670A LEU* 1.3 75.8 - - - +
672A ASN* 1.3 60.7 + - - +
674A SER* 3.9 4.0 - - - +
675A ALA* 2.8 31.5 + - - +
691A ILE* 4.0 13.3 - - + +
694A GLU* 2.7 45.1 + - + +
695A VAL* 3.4 33.0 - - + -
698A CYS* 3.9 9.8 - - + -
757A LEU* 4.4 7.2 - - + -
758A LEU* 4.0 2.8 - - + +
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Residues in contact with ASN 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A ASP* 2.6 33.8 + - - +
671A TYR* 1.3 76.9 - - - +
673A ASP* 1.3 62.8 + - - +
675A ALA* 3.7 4.1 - - - +
676A HIS* 2.8 33.3 + - - +
756A GLN* 3.0 26.0 + - - +
757A LEU* 3.5 10.5 - - - +
758A LEU* 2.8 31.6 + - - +
759A GLY 4.8 0.2 + - - -
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Residues in contact with ASP 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LYS* 2.6 35.7 + - - -
616A CYS 5.0 4.3 - - - +
617A ASP* 5.3 0.7 - - - +
618A LEU* 4.2 11.3 + - - +
619A SER* 3.4 23.9 - - - +
669A ASP* 4.0 4.7 - - - +
670A LEU* 3.3 19.4 + - - +
672A ASN* 1.3 78.5 - - - +
674A SER* 1.3 57.2 + - - +
676A HIS* 3.5 5.8 + - - +
677A TYR* 3.0 28.6 + - - +
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Residues in contact with SER 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LEU 4.8 0.9 + - - -
619A SER* 2.9 29.9 + - - -
621A LEU* 5.7 0.2 - - - +
622A TRP* 3.3 25.5 + - - +
623A PHE* 3.4 13.5 - - - -
670A LEU* 3.1 15.3 + - - +
671A TYR* 3.9 4.7 - - - -
673A ASP* 1.3 74.6 - - - +
675A ALA* 1.3 61.0 + - - +
677A TYR 3.3 0.5 + - - -
678A ALA 2.9 23.7 + - - -
691A ILE* 3.4 19.6 - - - +
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Residues in contact with ALA 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A TYR 2.8 19.5 + - - +
672A ASN* 3.7 3.8 - - - +
674A SER* 1.3 77.4 - - - +
676A HIS* 1.3 62.2 + - - +
678A ALA* 3.3 2.9 + - - +
679A LEU* 3.1 30.6 + - + +
688A TYR* 4.2 17.4 - - + -
691A ILE* 3.7 13.8 - - + +
758A LEU* 3.5 24.7 - - + -
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Residues in contact with HIS 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 5.3 11.9 + - - -
672A ASN 2.8 17.5 + - - +
673A ASP* 3.8 5.5 + - - +
675A ALA* 1.3 75.9 - - - +
677A TYR* 1.3 56.1 + - - +
679A LEU* 3.3 6.4 + - + -
680A THR* 2.7 57.8 + - + +
681A ARG* 3.4 27.4 + - - -
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Residues in contact with TYR 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLN* 5.2 5.9 + - - -
617A ASP* 4.1 14.6 - - - -
619A SER* 3.1 27.4 - - - -
620A GLN* 3.5 21.4 + - - -
623A PHE* 4.2 3.4 - + + -
673A ASP 3.0 17.7 + - - +
674A SER 3.7 4.9 - - - +
675A ALA 3.2 0.2 - - - -
676A HIS* 1.3 79.1 - - - +
678A ALA* 1.3 59.1 + - - +
680A THR* 4.1 4.3 - - - -
681A ARG* 2.9 60.5 + - + +
682A PHE* 3.1 41.4 + + - -
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Residues in contact with ALA 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A PHE* 4.1 11.0 - - + -
674A SER 2.9 17.2 + - - +
675A ALA* 3.3 5.6 + - - +
677A TYR* 1.3 76.3 - - - +
679A LEU* 1.3 58.4 + - - +
682A PHE* 3.9 10.0 - - - -
683A ASN 3.1 19.2 + - - -
684A LYS 3.2 15.5 + - - +
687A LEU* 3.9 25.1 - - + -
688A TYR* 4.3 9.6 - - + +
691A ILE* 4.2 8.3 - - + -
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Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675A ALA* 3.1 21.5 + - + +
676A HIS* 3.9 7.0 - - + +
677A TYR 3.2 0.2 - - - -
678A ALA* 1.3 81.3 - - - +
680A THR* 1.3 65.2 + - + +
681A ARG 3.8 0.2 - - - -
683A ASN* 3.8 19.1 - - - +
684A LYS 5.2 2.9 - - - +
685A GLN* 5.8 4.3 - - + -
688A TYR* 3.8 46.0 - - + -
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Residues in contact with THR 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A HIS* 2.7 43.4 + - + +
679A LEU* 1.3 87.7 - - + +
681A ARG* 1.3 92.5 + - - +
683A ASN* 4.6 4.3 - - - +
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Residues in contact with ARG 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.2 14.2 - - + +
610A GLU* 5.7 5.3 + - - +
613A GLN* 5.2 8.3 + - - -
614A GLN* 5.5 8.7 - - - +
676A HIS* 3.4 21.6 + - - -
677A TYR* 2.9 54.5 + - + +
680A THR* 1.3 103.5 + - - +
682A PHE* 1.3 66.0 + - + +
683A ASN* 3.3 4.6 + - - +
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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