Contacts of the helix formed by residues 633 - 644 (chain C) in PDB entry 1U0O
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 633 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595C SER* 4.2 4.5 + - - -
596C GLU* 5.5 2.6 - - - +
629C ARG 5.1 2.2 + - - +
630C MET* 2.9 16.9 + - - +
632C ARG* 1.3 89.7 + - - +
634C LEU* 1.3 63.8 + - - +
635C VAL 3.1 4.5 + - - -
636C ARG* 3.2 17.5 + - - +
637C TYR* 3.1 57.7 + - + -
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Residues in contact with LEU 634 (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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594C THR* 3.6 11.9 - - - +
595C SER* 3.4 38.1 - - - +
598C LEU* 3.9 16.4 - - + -
626C GLU* 4.1 0.7 - - - +
631C ALA* 3.1 21.6 + - + +
633C ASN* 1.3 76.7 - - - +
635C VAL* 1.3 60.4 + - - +
637C TYR* 4.1 1.4 - - - +
638C VAL* 2.9 32.0 + - - +
661C GLN* 3.5 47.8 - - + +
664C LEU* 3.9 13.2 - - + -
665C ILE* 4.0 15.9 - - + -
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Residues in contact with VAL 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 4.0 11.0 - - + +
49A LYS* 5.8 0.7 - - - +
114A LEU* 4.0 20.2 - - + -
292B LEU* 6.4 0.7 - - + -
631C ALA 4.5 1.0 + - - +
632C ARG 5.1 2.8 - - - +
633C ASN 3.2 1.4 - - - +
634C LEU* 1.3 75.0 - - - +
636C ARG* 1.3 56.6 + - - +
638C VAL* 3.2 2.7 + - - +
639C GLN* 2.7 34.2 + - + +
664C LEU* 3.3 39.0 - - + -
668C GLN* 3.7 28.4 - - - +
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Residues in contact with ARG 636 (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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107A GLU* 3.8 12.7 + - - -
109A ASP* 2.6 41.6 + - - +
110A LEU* 3.9 15.9 - - + +
114A LEU* 3.5 47.9 - - + +
602C LEU* 5.0 0.5 - - - +
632C ARG 5.6 1.1 + - - +
633C ASN* 3.2 20.6 + - - +
635C VAL* 1.3 80.4 - - - +
637C TYR* 1.3 88.1 + - + +
639C GLN* 3.8 2.7 - - - +
640C GLY* 2.8 24.4 + - - -
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Residues in contact with TYR 637 (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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595C SER* 3.3 31.0 - - - +
596C GLU* 5.1 4.0 - - - -
598C LEU* 4.2 12.3 - - + +
599C LYS* 3.6 45.7 + - + +
602C LEU* 4.1 16.5 - - + +
603C PHE* 4.3 7.9 - + - -
633C ASN* 3.1 49.6 + - + +
634C LEU* 4.2 2.5 - - - +
636C ARG* 1.3 95.2 + - + +
638C VAL* 1.3 61.4 + - - +
640C GLY* 3.3 0.9 + - - +
641C LEU* 3.0 35.5 + - - +
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Residues in contact with VAL 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C LEU* 3.9 18.6 - - + -
634C LEU 2.9 25.0 + - - +
635C VAL* 3.7 3.4 - - - +
637C TYR* 1.3 74.8 - - - +
639C GLN* 1.3 62.5 + - - +
641C LEU* 3.5 9.6 + - - +
642C LYS* 3.1 19.2 + - - +
646C VAL 5.2 0.3 - - - +
648C VAL* 4.3 7.4 - - + +
664C LEU 5.4 0.2 - - - +
665C ILE* 3.6 43.1 - - + +
668C GLN* 3.4 29.8 - - + +
672C ASN* 3.7 10.2 + - - +
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Residues in contact with GLN 639 (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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49A LYS* 2.4 35.8 + - - +
50A ASP* 5.0 3.0 + - - -
110A LEU* 4.4 17.2 + - + +
113A VAL* 4.5 15.5 - - + +
114A LEU* 4.8 5.6 - - + +
635C VAL* 2.7 19.4 + - + +
636C ARG* 3.8 7.6 - - - +
638C VAL* 1.3 77.1 - - - +
640C GLY* 1.3 64.5 + - - +
642C LYS* 3.0 40.8 + - - +
643C LYS* 3.0 31.7 + - + +
668C GLN* 3.4 12.8 - - + +
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Residues in contact with GLY 640 (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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110A LEU* 3.9 16.1 - - - +
602C LEU* 3.7 24.2 - - - +
636C ARG 2.8 18.9 + - - -
637C TYR 3.3 2.8 + - - -
639C GLN* 1.3 77.8 - - - +
641C LEU* 1.3 58.8 + - - +
642C LYS 3.3 0.7 + - - -
643C LYS* 3.3 14.5 + - - +
644C LYS* 3.3 11.4 + - - +
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Residues in contact with LEU 641 (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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598C LEU* 3.7 39.7 - - + +
601C THR* 4.1 11.2 - - + +
602C LEU* 3.5 39.0 - - + +
606C PHE* 4.7 0.9 - - + -
618C THR* 5.1 0.9 - - - +
637C TYR 3.0 21.0 + - - +
638C VAL* 3.8 6.1 - - - +
639C GLN 3.3 0.2 - - - -
640C GLY* 1.3 73.4 - - - +
642C LYS* 1.3 55.3 + - - +
644C LYS* 3.4 5.7 + - - -
646C VAL* 2.6 72.0 + - + +
648C VAL* 3.9 15.3 - - + -
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Residues in contact with LYS 642 (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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49A LYS* 4.9 3.6 - - - +
50A ASP* 4.2 21.6 + - - -
638C VAL 3.1 13.6 + - - +
639C GLN* 3.0 35.7 + - - +
641C LEU* 1.3 74.3 - - - +
643C LYS* 1.3 54.6 + - - +
644C LYS 2.9 4.3 - - - -
645C LYS* 2.6 28.8 + - - +
646C VAL 3.9 8.0 + - - +
668C GLN* 3.2 29.4 + - + +
669C ALA* 3.7 18.6 - - + +
670C PRO* 5.4 2.7 - - - -
671C GLU* 5.6 0.9 - - - -
672C ASN* 6.0 1.6 - - - +
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Residues in contact with LYS 643 (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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110A LEU* 4.0 46.1 - - + +
111A GLY 4.9 0.6 - - - +
639C GLN* 3.0 27.9 + - + +
640C GLY* 3.3 7.8 + - - +
642C LYS* 1.3 74.9 - - + +
644C LYS* 1.3 61.7 + - + +
645C LYS* 3.2 5.5 + - - +
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Residues in contact with LYS 644 (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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602C LEU* 3.8 29.3 + - + -
606C PHE* 3.1 26.5 + - + +
607C GLY* 3.1 16.0 + - - -
609C ILE* 4.0 29.1 - - + +
616C HIS* 4.1 5.5 + - - -
640C GLY 3.3 8.4 + - - +
641C LEU* 3.8 9.4 - - - +
642C LYS 2.8 1.6 + - - -
643C LYS* 1.3 79.0 - - + +
645C LYS* 1.3 74.6 + - - +
646C VAL* 3.4 15.7 + - + +
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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