Contacts of the helix formed by residues 625 - 635 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621D VAL* 3.1 21.7 - - - +
622D GLY 3.0 18.2 - - - -
624D GLY* 1.3 66.9 + - - -
626D TYR* 1.3 66.9 + - - +
627D ASN 3.3 1.0 + - - -
628D LEU* 3.4 15.2 + - - +
629D LYS* 3.6 18.4 + - - +
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Residues in contact with TYR 626 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B LEU* 3.9 30.5 + - + +
403B GLU* 4.8 12.1 - - + -
406B ILE* 3.8 32.8 - - + -
418B ILE* 4.5 6.2 - - - +
422B ASN* 3.9 23.2 + - - -
621D VAL 3.5 0.6 + - - -
623D PRO* 2.6 27.6 + - + +
624D GLY* 3.6 1.2 - - - -
625D GLY* 1.3 71.1 - - - -
627D ASN* 1.3 77.9 + - - +
629D LYS* 3.1 10.8 + - - +
630D LYS* 2.9 51.1 + - + +
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Residues in contact with ASN 627 (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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619D LYS 3.0 27.7 + - - -
620D PHE 3.3 18.6 + - - +
621D VAL 3.1 5.0 + - - +
622D GLY* 3.7 13.2 - - - +
623D PRO* 5.2 1.4 - - - +
626D TYR* 1.3 89.6 - - - +
628D LEU* 1.3 63.4 + - - +
630D LYS* 3.5 7.3 + - - +
631D LEU* 3.1 23.2 + - - +
663D PHE* 4.3 21.0 - - + -
667D ILE* 5.1 4.9 - - - +
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Residues in contact with LEU 628 (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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620D PHE* 3.7 41.5 - - + +
621D VAL* 3.6 32.7 + - + -
625D GLY* 3.4 7.4 + - - +
626D TYR 3.3 0.8 - - - -
627D ASN* 1.3 73.2 - - + +
629D LYS* 1.3 65.9 + - + +
631D LEU* 3.2 7.3 + - - +
632D GLN* 3.0 25.1 + - - +
637D VAL 4.9 0.7 - - - +
639D ILE* 4.2 32.9 + - + +
640D SER* 6.2 0.4 - - - -
641D GLN 6.1 0.4 - - - +
647D PHE* 4.2 14.1 - - + -
663D PHE* 5.2 3.4 - - + -
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Residues in contact with LYS 629 (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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403B GLU* 6.4 0.6 - - - +
406B ILE* 3.4 35.4 - - + +
418B ILE* 4.6 1.7 - - - +
624D GLY* 3.3 36.2 + - - -
625D GLY 3.6 10.7 + - - +
626D TYR* 3.1 5.1 + - - +
628D LEU* 1.3 77.3 - - + +
630D LYS* 1.3 63.3 + - - +
632D GLN* 3.3 10.8 + - - +
633D ALA* 3.1 22.4 + - - +
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Residues in contact with LYS 630 (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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406B ILE* 5.0 0.4 - - - +
418B ILE* 3.6 27.3 - - + +
420B ASP* 5.9 0.6 + - - -
626D TYR* 2.9 43.9 + - + +
627D ASN* 3.5 8.5 - - - +
629D LYS* 1.3 77.4 - - - +
631D LEU* 1.3 57.4 + - - +
633D ALA* 3.0 3.3 + - - +
634D GLU* 2.9 74.2 + - + +
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Residues in contact with LEU 631 (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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627D ASN 3.1 15.5 + - - +
628D LEU* 3.2 6.3 + - - +
630D LYS* 1.3 76.6 - - - +
632D GLN* 1.3 55.7 + - - +
634D GLU* 4.5 4.0 - - - +
635D THR* 2.7 77.7 + - + +
637D VAL* 3.7 15.7 - - + +
639D ILE* 3.9 23.8 - - + -
660D ALA* 4.1 16.6 - - + +
663D PHE* 3.4 45.5 - - + -
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Residues in contact with GLN 632 (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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112B ILE* 4.7 10.1 - - + +
410B GLN* 4.5 32.2 - - - +
411B VAL* 4.9 6.5 - - - +
414B ALA* 5.0 2.8 - - - +
403D GLU* 6.2 1.0 - - - +
628D LEU 3.0 16.1 + - - +
629D LYS* 3.7 9.2 - - - +
630D LYS 3.3 0.2 - - - -
631D LEU* 1.3 76.6 - - - +
633D ALA* 1.3 57.2 + - - +
636D GLY* 3.3 20.2 + - - -
637D VAL 3.1 21.7 + - - +
638D THR* 3.5 34.1 - - + +
639D ILE 4.5 6.2 + - - +
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Residues in contact with ALA 633 (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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108B ALA* 4.5 12.6 - - - +
410B GLN 5.7 1.1 - - - +
413B THR* 4.4 18.8 - - - +
414B ALA* 4.8 16.4 - - - +
417B GLY* 5.1 5.1 - - - -
418B ILE* 3.7 29.6 + - + +
629D LYS 3.1 11.6 + - - +
630D LYS 3.0 9.5 + - - +
632D GLN* 1.3 79.7 - - - +
634D GLU* 1.3 63.8 + - - +
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Residues in contact with GLU 634 (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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108B ALA* 4.6 5.4 - - - +
111B ARG* 5.2 2.1 + - - -
206B ARG* 4.3 19.4 + - - -
418B ILE* 4.4 19.1 + - + +
630D LYS* 2.9 56.6 + - + +
631D LEU* 4.3 2.9 - - - +
633D ALA* 1.3 81.2 - - + +
635D THR* 1.3 68.3 + - + +
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Residues in contact with THR 635 (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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108B ALA* 5.2 1.1 - - - -
111B ARG* 3.3 36.6 + - - +
631D LEU* 2.7 43.6 + - + +
634D GLU* 1.3 83.7 - - + +
636D GLY* 1.3 60.1 + - - +
637D VAL* 2.9 16.2 + - - +
652D PRO* 4.7 0.2 - - - +
656D ALA* 4.1 5.1 - - - +
659D GLU* 3.9 35.4 - - + +
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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