Contacts of the helix formed by residues 620 - 629 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614C LEU* 3.8 38.6 - - + +
617C ASN* 3.3 27.4 + - + +
619C SER* 1.3 95.4 + - - +
621C GLY* 1.3 62.7 + - - +
622C PRO 3.7 0.2 - - - -
623C LEU* 3.8 20.0 - - + +
624C GLN* 3.3 21.3 + - - +
1005C Y01 5.9 2.9 - - + -
636D LYS* 3.6 26.0 - - + -
639D VAL* 3.7 37.0 - - + -
640D ILE* 5.1 6.7 - - + +
643D MET* 5.9 0.2 - - + -
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Residues in contact with GLY 621 (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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614C LEU 3.8 10.1 + - - -
615C PRO* 4.0 10.1 - - - +
617C ASN 3.5 10.8 + - - -
620C PHE* 1.3 74.8 - - - +
622C PRO* 1.3 66.9 - - - +
624C GLN* 3.1 5.8 + - - +
625C ILE* 3.0 30.0 + - - +
742C TRP* 3.8 16.8 - - - -
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Residues in contact with PRO 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C ASN 4.4 0.2 - - - +
618C GLU 4.1 17.0 - - - +
619C SER* 4.5 7.4 - - - +
621C GLY* 1.3 86.9 - - - +
623C LEU* 1.3 60.4 + - + +
625C ILE* 3.7 8.9 - - + +
626C SER* 2.9 31.9 + - - -
738C ALA* 4.9 7.6 - - + +
739C ASP* 5.8 3.4 - - - +
742C TRP* 3.6 37.0 - - + +
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Residues in contact with LEU 623 (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 SER 3.4 22.2 - - - +
620C PHE* 3.8 17.7 + - + +
621C GLY 3.2 0.8 - - - -
622C PRO* 1.3 79.6 - - + +
624C GLN* 1.3 58.9 + - - +
626C SER* 3.2 9.0 + - - +
627C LEU* 2.9 31.9 + - - +
636D LYS* 3.3 55.6 - - + +
637D PHE* 4.0 24.5 - - + -
640D ILE* 4.2 17.0 - - + -
721D ASN* 4.8 1.2 + - - -
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Residues in contact with GLN 624 (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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611C ALA* 3.3 29.8 + - - +
614C LEU* 3.2 35.9 - - + +
615C PRO* 3.3 17.0 - - - +
620C PHE 3.3 10.0 + - - +
621C GLY* 3.1 9.3 + - - +
623C LEU* 1.3 76.8 - - - +
625C ILE* 1.3 63.0 + - + +
627C LEU* 3.4 4.6 + - - -
628C GLY* 2.9 23.7 + - - -
1003C S9Y 3.5 59.2 + - - +
640D ILE* 5.0 1.9 - - - +
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Residues in contact with ILE 625 (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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615C PRO* 6.1 3.1 - - + -
621C GLY 3.0 16.8 + - - +
622C PRO* 3.7 9.4 - - + +
623C LEU 3.3 0.2 - - - -
624C GLN* 1.3 79.5 - - + +
626C SER* 1.3 58.0 + - - +
628C GLY* 3.2 2.6 + - - -
629C ARG* 3.0 53.1 + - - +
738C ALA* 5.4 3.8 - - - +
741C GLU* 4.5 16.4 - - + +
742C TRP* 4.3 16.6 - - + +
745C ALA* 4.2 22.4 - - + -
1003C S9Y 4.9 9.9 - - - +
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Residues in contact with SER 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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622C PRO 2.9 19.4 + - - -
623C LEU* 3.2 16.6 + - - +
625C ILE* 1.3 75.8 - - - +
627C LEU* 1.3 56.2 + - - +
629C ARG* 3.5 19.1 - - - +
630C THR* 3.3 26.9 - - - +
637D PHE* 5.2 4.2 - - - -
721D ASN* 3.3 13.7 + - - +
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Residues in contact with LEU 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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623C LEU 2.9 15.7 + - - +
624C GLN* 3.8 5.8 - - - +
625C ILE 3.2 0.2 - - - -
626C SER* 1.3 75.8 + - - +
628C GLY* 1.3 63.6 + - - +
629C ARG 3.3 0.4 - - - -
630C THR* 3.4 8.7 + - - -
631C VAL* 3.4 20.2 - - + +
1003C S9Y 4.1 26.9 - - + +
1004C SBJ 5.8 5.4 - - + -
637D PHE* 5.7 3.8 - - + -
640D ILE* 4.0 38.8 - - + -
717D ILE* 5.1 8.1 - - + -
718D VAL* 4.7 20.6 - - + -
721D ASN* 3.5 27.6 - - + +
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Residues in contact with GLY 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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624C GLN 2.9 12.4 + - - -
625C ILE* 3.7 3.6 - - - -
627C LEU* 1.3 77.1 - - - +
629C ARG* 1.3 60.7 + - - +
630C THR 3.2 0.9 + - - -
631C VAL* 3.5 13.5 + - - +
632C LYS* 3.6 25.6 + - - +
1003C S9Y 3.7 30.8 + - - -
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Residues in contact with ARG 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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625C ILE* 3.0 38.2 + - - +
626C SER* 3.5 26.3 - - - +
628C GLY* 1.3 76.9 - - - +
630C THR* 1.3 63.5 + - + +
631C VAL 3.5 0.8 + - - -
632C LYS* 4.3 11.5 + - - +
633C ASP* 3.2 28.9 + - - +
730C SER* 6.0 1.8 - - - -
737C ASP 5.6 0.4 + - - -
738C ALA* 5.4 8.9 - - - +
741C 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