Contacts of the helix formed by residues 625 - 636 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621B VAL* 2.9 30.4 - - - +
622B GLY 2.8 6.5 + - - -
624B GLY* 1.3 78.8 - - - +
626B TYR* 1.3 62.3 + - - +
628B LEU* 3.2 18.2 + - - +
629B LYS* 3.2 18.3 + - - +
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Residues in contact with TYR 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B VAL 3.3 1.4 + - - -
623B PRO* 3.2 27.1 + - + +
624B GLY 3.2 1.0 - - - -
625B GLY* 1.3 77.2 - - - +
627B ASN* 1.3 78.0 + - - +
629B LYS* 3.1 14.2 + - + +
630B LYS* 2.9 51.3 + - + +
402C LEU* 3.9 32.5 + - + +
403C GLU* 4.7 15.7 - - + -
406C ILE* 3.6 26.7 - - + +
418C ILE* 4.6 3.8 - - - +
422C ASN* 4.1 20.6 + - - -
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Residues in contact with ASN 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B LYS 3.1 21.6 + - - -
620B PHE 3.2 15.3 + - - +
621B VAL 3.0 2.9 + - - +
622B GLY* 3.1 24.6 - - - -
623B PRO* 4.8 2.9 - - - +
626B TYR* 1.3 90.6 - - - +
628B LEU* 1.3 59.8 + - + +
630B LYS* 3.3 7.1 + - - +
631B LEU* 2.8 29.7 + - - +
663B PHE* 4.1 6.3 - - + -
667B ILE* 4.2 17.3 - - + +
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Residues in contact with LEU 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B PHE* 3.6 39.7 - - + +
621B VAL* 3.6 30.9 + - + +
625B GLY* 3.2 11.7 + - - +
627B ASN* 1.3 77.5 - - + +
629B LYS* 1.3 66.6 + - + +
631B LEU* 3.4 9.8 + - + +
632B GLN* 3.1 32.8 + - - +
639B ILE* 3.7 31.4 - - + +
647B PHE* 4.1 15.9 - - + -
667B ILE* 6.2 0.4 - - + -
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Residues in contact with LYS 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B GLY 3.5 23.6 - - - -
625B GLY* 3.2 11.0 + - - +
626B TYR* 3.1 14.7 + - + +
628B LEU* 1.3 77.6 - - + +
630B LYS* 1.3 61.8 + - - +
632B GLN* 3.3 14.7 + - - +
633B ALA* 3.1 22.2 + - - +
406C ILE* 3.7 34.8 - - + +
407C LYS 5.2 3.2 + - - +
408C SER* 4.8 12.7 + - - +
410C GLN* 4.8 1.6 - - - +
413C THR* 5.2 1.6 - - - +
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Residues in contact with LYS 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B TYR* 2.9 44.2 + - + +
627B ASN* 3.7 10.1 - - - +
629B LYS* 1.3 73.8 - - - +
631B LEU* 1.3 67.2 + - - +
633B ALA* 3.2 6.6 + - - +
634B GLU* 3.2 55.0 + - - +
663B PHE* 4.0 17.9 - - + -
406C ILE* 3.9 6.9 - - + +
418C ILE* 4.6 17.2 - - + +
420C ASP* 5.9 0.4 + - - -
422C ASN* 5.9 0.4 - - - +
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Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B ASN 2.8 18.1 + - - +
628B LEU* 3.6 10.1 - - + +
629B LYS 3.3 0.2 - - - -
630B LYS* 1.3 75.2 - - - +
632B GLN* 1.3 56.4 + - - +
634B GLU* 3.4 1.2 + - - -
635B THR* 2.7 60.8 + - + +
637B VAL* 3.9 11.7 - - + -
639B ILE* 4.0 28.0 - - + -
649B VAL* 5.9 0.9 - - + -
660B ALA* 4.0 9.6 - - + +
663B PHE* 3.2 40.1 - - + -
664B ILE* 4.3 24.5 - - + -
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Residues in contact with GLN 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B LEU* 3.1 19.9 + - - +
629B LYS* 3.6 13.0 - - - +
630B LYS 3.2 0.2 - - - -
631B LEU* 1.3 77.9 - - - +
633B ALA* 1.3 55.5 + - - +
636B GLY* 3.0 25.5 + - - -
637B VAL* 3.1 21.9 - - + +
638B THR* 3.5 7.8 - - - +
639B ILE* 2.9 44.7 + - + +
108C ALA* 5.3 0.2 - - - +
112C ILE* 4.7 3.8 - - - +
410C GLN* 2.8 47.4 + - - +
414C ALA* 5.0 1.2 - - - +
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Residues in contact with ALA 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B LYS 3.1 15.2 + - - +
630B LYS 3.2 5.3 + - - +
632B GLN* 1.3 78.8 - - - +
634B GLU* 1.3 60.4 + - - +
636B GLY 4.5 0.9 - - - -
108C ALA* 4.4 12.9 - - - +
410C GLN* 4.7 1.3 + - - +
413C THR* 4.0 18.8 - - + -
414C ALA* 4.7 17.3 - - - +
417C GLY* 5.0 5.9 - - - -
418C ILE* 3.8 28.0 + - + +
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Residues in contact with GLU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B LYS* 3.2 55.9 + - - +
631B LEU* 4.4 1.8 - - - +
633B ALA* 1.3 81.5 - - + +
635B THR* 1.3 67.0 + - + +
636B GLY 3.6 0.2 - - - -
659B GLU* 4.0 9.0 - - - +
663B PHE* 4.0 15.4 - - + -
108C ALA* 5.4 3.9 - - - +
111C ARG* 4.1 3.3 + - - -
206C ARG* 5.2 6.8 + - - -
418C ILE* 4.3 14.6 - - + +
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Residues in contact with THR 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B LEU* 2.7 38.6 + - + +
634B GLU* 1.3 83.0 - - + +
636B GLY* 1.3 63.5 + - - +
637B VAL* 3.2 29.8 + - - +
656B ALA* 3.4 12.5 - - - +
659B GLU* 3.9 30.3 - - + +
663B PHE* 4.6 5.8 - - + -
108C ALA* 5.1 1.1 - - - -
111C ARG* 3.1 32.4 + - - +
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Residues in contact with GLY 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B GLN 3.0 19.0 + - - -
633B ALA 4.5 0.6 - - - -
634B GLU 3.6 1.2 - - - +
635B THR* 1.3 79.3 + - - +
637B VAL* 1.3 61.7 + - - +
638B THR* 4.8 0.7 + - - -
650B PHE* 5.3 1.0 - - - -
652B PRO* 3.0 24.0 - - - +
108C ALA* 4.4 4.9 - - - +
111C ARG* 4.3 7.0 - - - -
112C ILE* 3.3 30.5 - - - +
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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