Contacts of the helix formed by residues 669 - 679 (chain D) in PDB entry 4OIR
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 ASN 669 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662D GLU* 3.3 18.6 - - - +
667D ALA* 3.3 4.9 - - - +
668D PRO* 1.3 89.3 - - - +
670D VAL* 1.3 65.2 + - - +
671D LYS* 3.1 29.3 + - - +
672D ALA* 3.2 10.8 + - - +
673D ALA* 3.2 20.8 + - - +
349F LEU* 6.5 0.4 - - + -
417F LYS* 5.0 5.4 + - + +
420F ASP* 3.1 33.7 + - - +
421F PHE* 5.2 11.3 - - + -
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Residues in contact with VAL 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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1067C TYR* 5.0 2.0 - - - +
1071C ILE* 4.1 43.7 - - + +
658D LEU* 3.9 33.5 - - + +
659D LYS* 5.5 0.2 - - - -
662D GLU* 3.1 19.6 + - + +
669D ASN* 1.3 76.1 - - - +
671D LYS* 1.3 60.9 + - - +
673D ALA* 2.9 24.1 + - - +
674D ARG* 2.9 14.3 + - + +
349F LEU* 4.4 22.2 - - + +
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Residues in contact with LYS 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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669D ASN* 3.1 10.6 + - - +
670D VAL* 1.3 81.5 - - - +
672D ALA* 1.3 58.2 + - - +
674D ARG* 3.3 7.8 + - + +
675D ARG* 2.9 39.6 + - + +
346F THR* 4.0 35.9 - - + +
349F LEU* 5.8 1.5 - - + +
420F ASP* 3.2 31.6 + - + +
421F PHE* 3.5 23.5 + - + +
423F ASP* 2.8 29.0 + - - +
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Residues in contact with ALA 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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667D ALA* 4.5 1.3 - - + -
668D PRO* 3.9 19.7 - - + -
669D ASN* 3.2 27.5 + - - +
670D VAL 3.2 0.2 - - - -
671D LYS* 1.3 78.6 - - - +
673D ALA* 1.3 58.5 + - - +
675D ARG* 3.4 18.6 + - - +
676D MET* 2.9 30.2 + - - +
420F ASP* 3.8 12.8 + - - +
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Residues in contact with ALA 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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658D LEU* 3.7 20.0 - - + +
661D MET* 3.8 20.3 - - + +
667D ALA* 3.7 17.7 - - + +
669D ASN 3.2 10.4 + - - +
670D VAL* 2.9 11.2 + - - +
672D ALA* 1.3 79.5 - - - +
674D ARG* 1.3 57.8 + - - +
676D MET* 3.2 9.1 + - - +
677D LEU* 2.9 31.9 + - - +
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Residues in contact with ARG 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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1009C SER* 4.3 10.1 + - - -
1010C THR* 4.4 7.1 + - - -
1067C TYR* 2.7 32.7 + - - -
651D GLU* 5.5 0.4 + - - -
654D LYS* 3.6 36.1 + - - +
655D PRO 5.5 0.2 - - - -
658D LEU* 3.4 29.2 - - + +
670D VAL* 2.9 13.2 + - + +
671D LYS* 3.7 10.8 - - - +
673D ALA* 1.3 74.5 - - - +
675D ARG* 1.3 59.5 + - - +
677D LEU* 3.1 6.0 + - - +
678D GLU* 2.9 42.4 + - + +
342F VAL* 3.5 38.5 - - - +
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Residues in contact with ARG 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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671D LYS* 2.9 28.8 + - + +
672D ALA* 3.8 18.2 + - - +
674D ARG* 1.3 76.5 - - - +
676D MET* 1.3 60.8 + - - +
678D GLU* 3.6 34.8 + - - +
679D ARG* 4.4 3.8 + - - +
682D ASP* 4.5 5.9 - - - +
420F ASP* 3.4 47.9 + - - +
423F ASP* 5.9 2.8 - - - +
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Residues in contact with MET 676 (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 MET* 4.8 6.5 - - - +
666D ILE* 3.8 35.2 - - + +
667D ALA* 4.8 3.1 - - - -
672D ALA 2.9 17.6 + - - +
673D ALA* 3.3 13.9 - - - +
674D ARG 3.1 0.2 - - - -
675D ARG* 1.3 78.7 - - - +
677D LEU* 1.3 63.8 + - + +
679D ARG 3.8 1.0 - - - +
682D ASP* 3.2 43.1 - - + +
684D LYS* 3.6 42.4 - - + +
687D VAL* 3.9 10.8 - - + -
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Residues in contact with LEU 677 (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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650D LEU* 4.3 23.3 - - + +
654D LYS* 3.8 28.6 + - + +
657D LEU* 3.6 19.7 - - + -
658D LEU* 4.4 6.7 - - + -
661D MET* 3.6 30.1 - - + -
673D ALA 2.9 16.5 + - - +
674D ARG* 3.1 5.3 + - - +
676D MET* 1.3 83.3 - - + +
678D GLU* 1.3 65.1 + - - +
679D ARG 3.3 8.1 - - - +
683D ILE* 4.5 22.8 - - + +
687D VAL* 4.7 17.5 - - + -
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Residues in contact with GLU 678 (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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751C PRO* 4.6 4.7 - - - +
752C GLY* 4.9 4.5 - - - -
654D LYS* 5.0 4.5 - - - +
674D ARG* 2.9 27.7 + - + +
675D ARG* 3.6 34.5 + - - +
676D MET 3.4 1.0 - - - -
677D LEU* 1.3 79.7 - - - +
679D ARG* 1.3 65.1 + - + +
680D GLN 3.9 0.9 + - - -
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Residues in contact with ARG 679 (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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732C ALA* 4.3 18.0 + - - +
733C ALA* 4.3 28.4 + - - +
751C PRO 4.3 6.3 - - - +
752C GLY* 4.6 16.2 + - - +
753C ASP* 3.1 26.9 + - - +
791C ARG* 6.0 2.9 - - - +
675D ARG 4.4 3.9 + - - +
676D MET 4.4 0.6 + - - -
677D LEU 3.3 11.5 - - - +
678D GLU* 1.3 80.7 - - + +
680D GLN* 1.3 63.5 + - - +
681D ARG* 3.4 30.8 - - + +
682D ASP* 3.3 40.5 + - - +
683D ILE* 3.6 6.9 - - - +
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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
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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