Contacts of the helix formed by residues 625 - 636 (chain C) in PDB entry 3U1K
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 GLY 625 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621C VAL* 3.2 26.1 - - - +
622C GLY 3.0 6.0 + - - -
623C PRO 2.9 2.6 + - - -
624C GLY* 1.3 77.7 - - - +
626C TYR* 1.3 66.0 + - - +
628C LEU* 3.1 21.9 + - - +
629C LYS* 3.3 17.4 + - - +
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Residues in contact with TYR 626 (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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621C VAL 3.4 1.2 + - - -
623C PRO* 2.9 26.8 + - + +
624C GLY 3.3 1.8 - - - -
625C GLY* 1.3 76.2 - - - +
627C ASN* 1.3 77.9 + - - +
629C LYS* 2.9 21.3 + - - +
630C LYS* 2.9 43.9 + - + +
402D LEU* 3.9 28.6 + - + +
403D GLU* 4.7 14.6 - - + -
406D ILE* 3.3 29.3 - - + +
418D ILE* 4.5 6.8 - - - +
422D ASN* 4.0 20.6 + - - -
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Residues in contact with ASN 627 (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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619C LYS 3.0 27.3 + - - -
620C PHE 3.2 12.5 + - - +
621C VAL 2.9 18.3 + - - +
622C GLY* 3.8 10.6 - - - +
623C PRO* 5.5 1.0 - - - +
626C TYR* 1.3 89.0 - - - +
628C LEU* 1.3 55.7 + - + +
630C LYS* 3.8 4.0 - - - +
631C LEU* 2.9 30.9 + - - +
663C PHE* 3.8 9.7 - - + -
667C ILE* 3.9 26.2 - - + +
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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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620C PHE* 3.7 35.0 - - + +
621C VAL* 3.6 21.5 + - + -
625C GLY* 3.1 14.1 + - - +
627C ASN* 1.3 76.9 - - - +
629C LYS* 1.3 66.0 + - + +
631C LEU* 3.4 8.2 + - + +
632C GLN* 3.1 31.7 + - - +
639C ILE* 3.7 32.7 - - + +
641C GLN* 5.3 5.6 - - + +
647C PHE* 4.1 18.4 - - + -
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Residues in contact with LYS 629 (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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624C GLY 4.0 16.3 + - - -
625C GLY* 3.4 15.0 - - - +
626C TYR* 2.9 9.9 + - - +
628C LEU* 1.3 78.6 - - + +
630C LYS* 1.3 63.6 + - - +
632C GLN* 3.3 17.9 + - - +
633C ALA* 3.1 22.3 + - - +
406D ILE* 3.9 31.6 - - + +
407D LYS 4.9 7.4 + - - +
408D SER* 5.1 12.8 + - - +
410D GLN* 5.9 3.8 - - + +
413D THR* 5.2 2.7 - - + +
418D ILE* 4.8 0.4 - - - -
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Residues in contact with LYS 630 (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 TYR* 2.9 46.5 + - + +
627C ASN* 3.9 4.9 - - - +
629C LYS* 1.3 76.9 - - - +
631C LEU* 1.3 57.8 + - - +
633C ALA* 3.2 1.2 + - - +
634C GLU* 2.8 65.4 + - + +
663C PHE* 4.4 11.7 - - + -
406D ILE* 4.3 0.8 - - - +
418D ILE* 3.8 29.6 - - + +
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Residues in contact with LEU 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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620C PHE* 5.5 1.3 - - + -
627C ASN 2.9 19.1 + - - +
628C LEU* 3.5 7.9 - - + +
630C LYS* 1.3 77.5 - - - +
632C GLN* 1.3 62.8 + - + +
634C GLU* 4.0 0.2 - - - -
635C THR* 2.9 43.7 + - + +
637C VAL* 4.0 10.1 - - + -
639C ILE* 4.2 31.2 - - + -
649C VAL* 5.7 1.1 - - + -
660C ALA* 3.9 15.7 - - + +
663C PHE* 3.6 46.4 - - + -
664C ILE* 4.2 21.8 - - + -
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Residues in contact with GLN 632 (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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628C LEU* 3.1 17.2 + - - +
629C LYS* 3.3 19.6 + - - +
631C LEU* 1.3 74.6 - - - +
633C ALA* 1.3 56.2 + - - +
636C GLY* 2.7 31.9 + - - -
637C VAL* 3.1 24.6 - - + +
638C THR* 3.5 7.1 - - - +
639C ILE* 2.7 45.5 + - + +
108D ALA* 5.2 0.3 - - - +
112D ILE* 5.1 2.3 - - - +
410D GLN* 3.4 40.7 + - + +
414D ALA* 5.3 1.8 - - - +
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Residues in contact with ALA 633 (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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629C LYS 3.1 16.2 + - - +
630C LYS 3.2 4.9 + - - +
632C GLN* 1.3 77.2 - - - +
634C GLU* 1.3 63.5 + - + +
108D ALA* 4.2 15.8 - - - +
410D GLN* 5.7 1.1 - - - +
413D THR* 3.9 26.2 - - + +
414D ALA* 4.8 17.6 - - - +
417D GLY* 5.1 3.7 - - - -
418D ILE* 4.0 20.2 - - + +
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Residues in contact with GLU 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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630C LYS* 2.8 55.4 + - + +
631C LEU 4.1 1.8 - - - +
633C ALA* 1.3 81.7 - - + +
635C THR* 1.3 66.1 + - + +
659C GLU* 4.3 6.1 - - - +
663C PHE* 3.6 19.7 - - + -
108D ALA* 5.4 2.9 - - - +
206D ARG* 4.3 11.8 + - - -
418D ILE* 5.9 4.1 - - + +
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Residues in contact with THR 635 (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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631C LEU* 2.9 28.8 + - + +
634C GLU* 1.3 84.9 - - + +
636C GLY* 1.3 61.5 + - - +
637C VAL* 3.2 29.6 - - - +
656C ALA* 3.9 11.2 - - - +
659C GLU* 3.8 35.4 - - + +
660C ALA 3.9 1.1 - - - +
663C PHE* 4.5 5.6 - - + -
108D ALA* 5.1 2.0 - - - -
111D ARG* 2.8 35.1 + - - +
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Residues in contact with GLY 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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632C GLN 2.7 17.2 + - - -
633C ALA 4.3 0.8 + - - -
634C GLU 3.6 1.2 - - - -
635C THR* 1.3 79.8 + - - +
637C VAL* 1.3 62.9 + - - +
638C THR* 5.1 0.2 + - - -
650C PHE* 5.7 0.3 - - - -
652C PRO* 3.4 25.4 - - - +
108D ALA* 4.2 10.3 - - - +
111D ARG* 4.0 3.7 - - - +
112D ILE* 3.6 27.4 - - - +
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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