Contacts of the helix formed by residues 620 - 629 (chain D) in PDB entry 6UZA
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 PHE 620 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636A LYS* 3.6 25.8 - - + -
639A VAL* 3.7 39.5 - - + -
640A ILE* 5.1 6.2 - - + +
643A MET* 5.9 0.4 - - + -
614D LEU* 3.8 39.7 - - + +
617D ASN* 3.3 27.1 + - - +
619D SER* 1.3 94.6 + - - +
621D GLY* 1.3 63.1 + - - +
622D PRO 3.7 0.4 - - - -
623D LEU* 3.8 19.3 - - + +
624D GLN* 3.3 21.7 + - - +
1004D Y01 5.9 3.1 - - + -
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Residues in contact with GLY 621 (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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614D LEU 3.8 10.3 + - - -
615D PRO* 4.0 10.3 - - - +
617D ASN 3.5 10.6 + - - -
620D PHE* 1.3 75.6 - - - +
622D PRO* 1.3 68.6 - - - +
624D GLN* 3.1 6.2 + - - +
625D ILE* 3.0 29.6 + - - +
742D TRP* 3.8 17.3 - - - -
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Residues in contact with PRO 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D GLU 4.1 16.8 - - - +
619D SER* 4.5 7.4 - - - +
621D GLY* 1.3 87.8 - - - +
623D LEU* 1.3 61.4 + - + +
625D ILE* 3.7 9.0 - - + +
626D SER* 2.9 31.1 + - - -
738D ALA* 4.9 7.9 - - + +
739D ASP* 5.8 2.9 - - - +
742D TRP* 3.6 37.2 - - + +
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Residues in contact with LEU 623 (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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636A LYS* 3.3 55.0 - - + +
637A PHE* 4.0 25.6 - - + +
640A ILE* 4.2 18.2 - - + -
721A ASN* 4.8 1.0 + - - -
619D SER 3.4 21.8 - - - +
620D PHE* 3.8 17.9 + - + +
621D GLY 3.2 0.8 - - - -
622D PRO* 1.3 80.6 - - + +
624D GLN* 1.3 57.9 + - - +
626D SER* 3.2 7.7 + - - +
627D LEU* 2.9 32.6 + - - +
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Residues in contact with GLN 624 (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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640A ILE* 5.0 2.2 - - - +
611D ALA* 3.3 29.8 + - - +
614D LEU* 3.2 35.1 - - + +
615D PRO* 3.3 17.6 - - - +
620D PHE 3.3 10.6 + - - +
621D GLY* 3.1 10.1 + - - +
623D LEU* 1.3 77.2 - - - +
625D ILE* 1.3 61.3 + - + +
627D LEU* 3.8 4.7 - - - -
628D GLY* 2.9 23.9 + - - -
1003D S9Y 3.5 60.6 + - - +
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Residues in contact with ILE 625 (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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615D PRO* 6.1 2.5 - - + -
621D GLY 3.0 16.6 + - - +
622D PRO* 3.7 9.2 - - + +
623D LEU 3.3 0.2 - - - -
624D GLN* 1.3 79.3 - - + +
626D SER* 1.3 56.9 + - - +
628D GLY* 3.2 2.3 + - - -
629D ARG* 3.0 53.0 + - - +
738D ALA* 5.4 4.5 - - - +
741D GLU* 4.5 16.4 - - + +
742D TRP* 4.3 17.7 - - + +
745D ALA* 4.2 23.1 - - + -
1003D S9Y 4.9 10.5 - - - +
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Residues in contact with SER 626 (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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637A PHE* 5.2 3.8 - - - -
721A ASN* 3.3 13.6 + - - +
622D PRO 2.9 18.8 + - - -
623D LEU* 3.2 15.9 + - - +
625D ILE* 1.3 76.4 - - - +
627D LEU* 1.3 57.3 + - - +
629D ARG* 3.5 19.4 - - - +
630D THR* 3.3 27.0 - - - +
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Residues in contact with LEU 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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637A PHE* 5.7 3.1 - - + -
640A ILE* 4.0 38.8 - - + -
717A ILE* 5.1 7.9 - - + -
718A VAL* 4.7 20.0 - - + -
721A ASN* 3.5 28.5 - - + +
1005A SBJ 5.8 4.5 - - + -
623D LEU* 2.9 16.9 + - + +
624D GLN* 3.8 5.4 - - - +
626D SER* 1.3 75.7 - - - +
628D GLY* 1.3 64.0 + - - +
629D ARG 3.3 0.2 - - - -
630D THR* 3.4 7.8 + - - -
631D VAL* 3.4 20.5 - - + +
1003D S9Y 4.1 26.7 - - + +
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Residues in contact with GLY 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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624D GLN 2.9 11.8 + - - -
625D ILE* 3.7 3.4 - - - -
627D LEU* 1.3 78.1 - - - +
629D ARG* 1.3 61.9 + - - +
630D THR 3.4 0.9 + - - -
631D VAL* 3.5 13.6 + - - +
632D LYS* 3.6 24.2 + - - +
1003D S9Y 3.7 30.4 + - - -
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Residues in contact with ARG 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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625D ILE* 3.0 37.5 + - - +
626D SER* 3.5 25.2 - - - +
627D LEU 3.3 0.2 - - - -
628D GLY* 1.3 78.4 - - - +
630D THR* 1.3 62.7 + - + +
631D VAL 3.5 0.7 - - - -
632D LYS* 4.3 11.2 + - - +
633D ASP* 3.2 28.4 + - - +
730D SER* 6.0 1.6 - - - -
737D ASP 5.6 0.6 + - - -
738D ALA* 5.4 8.7 - - - +
741D GLU* 4.6 11.3 - - - +
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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