Contacts of the helix formed by residues 627 - 631 (chain C) in PDB entry 4YFI
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 627 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C GLY* 1.3 73.0 - - - -
628C LEU* 1.3 63.4 + - - +
629C ARG* 3.0 20.5 + - - +
630C TRP* 3.3 34.5 + - + +
631C MET* 3.9 12.1 + - - +
588D ASP* 3.3 10.8 + - - +
590D ASN* 4.2 18.7 + - - +
592D HIS* 5.3 8.4 + - + -
670D PRO* 4.4 16.2 - - - +
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Residues in contact with LEU 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C GLY 4.7 4.7 - - - +
627C ASN* 1.3 72.7 + - - +
629C ARG* 1.3 63.6 + - - +
630C TRP 3.2 3.8 + - - -
631C MET* 3.3 45.9 + - + +
636C PHE* 4.0 19.1 - - + -
639C CYS* 4.4 9.6 - - + -
670D PRO* 4.0 20.5 - - + +
671D ALA* 3.7 30.7 - - + +
674D ASP* 3.5 21.5 - - + +
677D MET* 4.6 0.3 - - - +
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Residues in contact with ARG 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627C ASN* 3.0 13.4 + - - +
628C LEU* 1.3 77.7 - - - +
630C TRP* 1.3 81.4 + - + +
653D LEU* 3.6 6.4 - - - +
663D ILE* 3.3 29.4 - - - +
664D PRO* 3.1 32.8 + - + +
665D PHE* 3.1 22.3 + - + +
666D ALA* 4.5 1.8 + - - +
668D LEU 3.0 21.6 + - - -
669D LYS* 3.7 0.6 - - - +
670D PRO* 3.3 43.1 - - + +
673D ALA* 4.3 11.6 - - + +
677D MET* 3.4 19.8 - - - +
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Residues in contact with TRP 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627C ASN* 3.3 40.1 + - + +
628C LEU 3.2 0.4 - - - -
629C ARG* 1.3 101.4 - - + +
631C MET* 1.3 64.2 + - - +
548D PHE* 4.2 19.1 - + - -
588D ASP 6.2 0.2 - - - -
589D LEU 3.6 15.0 - - - +
590D ASN* 3.3 29.0 - - + +
591D SER* 3.4 20.6 - - - -
592D HIS* 4.2 13.5 - + - -
650D SER* 3.0 29.3 + - - -
653D LEU* 3.8 24.1 - - + +
654D CYS* 3.9 15.8 - - - +
657D GLU* 2.7 30.1 + - - -
663D ILE* 4.9 1.6 - - + -
664D PRO* 4.2 13.3 - - + +
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Residues in contact with MET 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C GLY* 4.0 30.5 - - - +
627C ASN 3.9 11.1 + - - +
628C LEU* 3.3 38.2 + - + +
630C TRP* 1.3 78.7 - - - +
632C ALA* 1.3 68.3 + - - +
633C PRO 3.7 0.5 - - - -
635C VAL* 4.0 17.3 - - + -
636C PHE* 3.6 34.0 - - + +
639C CYS* 3.7 16.6 - - - -
587D ARG 5.8 5.8 - - - +
649D PHE* 3.3 16.2 - - - -
650D SER* 4.4 3.1 - - - -
674D ASP* 5.3 1.1 - - + +
677D MET* 3.7 11.1 - - - +
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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