Contacts of the helix formed by residues 620 - 629 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A LEU* 3.8 39.2 - - + +
617A ASN* 3.3 27.3 + - - +
619A SER* 1.3 94.7 + - - +
621A GLY* 1.3 63.0 + - - +
622A PRO 3.7 0.4 - - - -
623A LEU* 3.8 19.2 - - + +
624A GLN* 3.3 21.1 + - - +
1004A Y01 5.9 2.9 - - + -
636B LYS* 3.6 26.2 - - + -
639B VAL* 3.7 37.2 - - + -
640B ILE* 5.1 6.2 - - + +
643B MET* 6.1 0.2 - - + -
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Residues in contact with GLY 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A LEU 3.8 9.5 + - - -
615A PRO* 4.0 10.3 - - - +
617A ASN 3.5 11.2 + - - -
620A PHE* 1.3 76.4 - - - +
622A PRO* 1.3 68.0 - - - +
624A GLN* 3.1 6.4 + - - +
625A ILE* 3.0 29.6 + - - +
742A TRP* 3.8 17.0 - - - -
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Residues in contact with PRO 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A GLU 4.1 16.6 - - - +
619A SER* 4.5 7.6 - - - +
621A GLY* 1.3 87.5 - - - +
623A LEU* 1.3 63.0 + - + +
625A ILE* 3.7 9.5 - - + +
626A SER* 2.9 31.0 + - - -
738A ALA* 4.9 7.6 - - + +
739A ASP* 5.8 3.1 - - - +
742A TRP* 3.6 37.9 - - + +
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Residues in contact with LEU 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A SER 3.4 22.2 - - - +
620A PHE* 3.8 17.9 + - + +
621A GLY 3.2 0.8 - - - -
622A PRO* 1.3 81.6 - - + +
624A GLN* 1.3 58.0 + - - +
626A SER* 3.2 8.1 + - - +
627A LEU* 2.9 32.4 + - + +
636B LYS* 3.3 55.4 - - + +
637B PHE* 4.0 24.2 - - + -
640B ILE* 4.2 17.3 - - + -
721B ASN* 4.8 1.2 + - - -
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Residues in contact with GLN 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A ALA* 3.3 29.9 + - - +
614A LEU* 3.2 36.2 - - + +
615A PRO* 3.3 16.2 - - - +
620A PHE 3.3 10.2 + - - +
621A GLY 3.1 9.9 + - - +
623A LEU* 1.3 76.6 - - - +
625A ILE* 1.3 61.0 + - + +
627A LEU* 3.4 5.1 + - - -
628A GLY* 2.9 24.1 + - - -
1002A S9Y 3.5 59.8 + - - +
640B ILE* 5.0 2.2 - - - +
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Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A PRO* 6.1 2.9 - - + -
621A GLY 3.0 16.8 + - - +
622A PRO* 3.7 9.6 - - + +
623A LEU 3.3 0.2 - - - -
624A GLN* 1.3 79.8 - - + +
626A SER* 1.3 56.0 + - - +
628A GLY* 3.2 2.5 + - - -
629A ARG* 3.0 53.5 + - - +
738A ALA* 5.4 4.5 - - - +
741A GLU* 4.5 16.2 - - + +
742A TRP* 4.3 16.8 - - + +
745A ALA* 4.2 22.9 - - + -
1002A S9Y 4.9 10.3 - - - +
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Residues in contact with SER 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A PRO 2.9 19.4 + - - -
623A LEU* 3.2 16.8 + - - +
625A ILE* 1.3 75.2 - - - +
627A LEU* 1.3 58.3 + - - +
629A ARG* 3.5 19.4 - - - +
630A THR* 3.3 26.7 - - - +
637B PHE* 5.2 3.8 - - - -
721B ASN* 3.3 13.8 + - - +
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Residues in contact with LEU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A LEU 2.9 16.4 + - - +
624A GLN* 3.8 5.6 - - - +
626A SER* 1.3 74.8 - - - +
628A GLY* 1.3 64.5 + - - +
629A ARG 3.3 0.4 - - - -
630A THR* 3.4 8.0 + - - +
631A VAL* 3.4 20.3 - - + +
1002A S9Y 4.1 26.7 - - + +
1003A SBJ 5.8 4.9 - - + -
637B PHE* 5.7 3.4 - - + -
640B ILE* 4.0 39.0 - - + -
717B ILE* 5.1 7.6 - - + -
718B VAL* 4.7 20.6 - - + -
721B ASN* 3.5 27.8 - - + +
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Residues in contact with GLY 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A GLN 2.9 11.5 + - - -
625A ILE 3.2 3.1 + - - -
627A LEU* 1.3 78.4 - - - +
629A ARG* 1.3 60.7 + - - +
630A THR 3.2 1.1 + - - -
631A VAL* 3.5 13.3 + - - +
632A LYS* 3.6 25.7 + - - +
1002A S9Y 3.7 30.5 - - - -
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Residues in contact with ARG 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A ILE* 3.0 38.1 + - - +
626A SER* 3.5 26.4 - - - +
628A GLY* 1.3 77.6 - - - +
630A THR* 1.3 63.7 + - + +
631A VAL 3.5 0.8 + - - -
632A LYS* 4.3 10.8 + - - +
633A ASP* 3.2 29.3 + - - +
730A SER* 6.0 1.8 - - - -
737A ASP 6.1 0.2 - - - -
738A ALA* 5.4 9.1 - - - +
741A GLU* 4.6 11.9 - - - +
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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