Contacts of the helix formed by residues 620 - 629 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B LEU* 3.8 40.2 - - + +
617B ASN* 3.3 28.7 + - + +
619B SER* 1.3 96.0 + - - +
621B GLY* 1.3 63.7 + - - +
622B PRO 3.7 0.4 - - - -
623B LEU* 3.8 19.2 - - + +
624B GLN* 3.3 21.1 + - - +
1005B Y01 5.9 2.7 - - + -
636C LYS* 3.6 26.5 - - + -
639C VAL* 3.7 36.6 - - + -
640C ILE* 5.1 6.5 - - + -
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Residues in contact with GLY 621 (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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614B LEU 3.8 10.4 + - - -
615B PRO* 4.0 9.8 - - - +
617B ASN 3.5 10.6 + - - -
620B PHE* 1.3 75.8 - - - +
622B PRO* 1.3 68.3 - - - +
624B GLN* 3.1 6.1 + - - +
625B ILE* 3.0 29.8 + - - +
742B TRP* 3.8 17.3 - - - -
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Residues in contact with PRO 622 (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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618B GLU 4.1 16.6 - - - +
619B SER* 4.5 7.9 - - - +
621B GLY* 1.3 87.4 - - - +
623B LEU* 1.3 61.5 + - + +
625B ILE* 3.4 10.0 + - + +
626B SER* 2.9 31.2 + - - -
738B ALA* 4.9 8.1 - - + +
739B ASP* 5.8 2.9 - - - +
742B TRP* 3.6 37.2 - - + +
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Residues in contact with LEU 623 (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 SER 3.4 22.4 - - - +
620B PHE* 3.8 17.9 + - + +
621B GLY 3.2 1.2 - - - -
622B PRO* 1.3 83.1 - - + +
624B GLN* 1.3 57.2 + - - +
626B SER* 3.2 7.7 + - - +
627B LEU* 2.9 32.5 + - - +
636C LYS* 3.3 55.0 - - + +
637C PHE* 4.0 25.9 - - + +
640C ILE* 4.2 18.2 - - + -
721C ASN* 4.8 1.0 + - - -
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Residues in contact with GLN 624 (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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611B ALA* 3.3 30.4 + - - +
614B LEU* 3.2 35.9 - - + +
615B PRO* 3.3 16.3 - - - +
620B PHE 3.3 10.6 + - - +
621B GLY 3.1 9.8 + - - +
623B LEU* 1.3 76.8 - - - +
625B ILE* 1.3 61.1 + - + +
627B LEU* 3.8 4.4 - - - -
628B GLY* 2.9 24.3 + - - -
1003B S9Y 3.5 59.7 + - - +
640C ILE* 5.0 2.4 - - - +
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Residues in contact with ILE 625 (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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615B PRO* 6.1 3.1 - - + -
621B GLY 3.0 17.0 + - - +
622B PRO* 3.7 9.4 - - + +
623B LEU 3.3 0.2 - - - -
624B GLN* 1.3 80.4 - - + +
626B SER* 1.3 58.1 + - - +
628B GLY* 3.2 2.3 + - - -
629B ARG* 3.0 53.2 + - - +
738B ALA* 5.4 3.8 - - - +
741B GLU* 4.5 15.3 - - + +
742B TRP* 4.3 16.4 - - + +
745B ALA* 4.2 22.4 - - + -
1003B S9Y 4.9 9.9 - - - +
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Residues in contact with SER 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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622B PRO 2.9 18.5 + - - -
623B LEU* 3.2 16.3 + - - +
625B ILE* 1.3 77.3 - - - +
627B LEU* 1.3 57.2 + - - +
629B ARG* 3.5 18.6 - - - +
630B THR* 3.3 27.2 - - - +
637C PHE* 5.2 4.0 - - - -
721C ASN* 3.3 13.3 + - - +
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Residues in contact with LEU 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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623B LEU 2.9 16.4 + - - +
624B GLN* 3.8 4.9 - - - +
625B ILE 3.2 0.2 - - - -
626B SER* 1.3 75.3 + - - +
628B GLY* 1.3 64.8 + - - +
629B ARG 3.3 0.4 - - - -
630B THR* 3.4 8.4 + - - -
631B VAL* 3.4 20.5 - - + +
1003B S9Y 4.1 26.0 - - + +
1004B SBJ 5.8 5.2 - - + -
637C PHE* 5.7 2.9 - - + -
640C ILE* 4.0 38.6 - - + -
717C ILE* 5.1 7.6 - - + -
718C VAL* 4.7 21.8 - - + -
721C ASN* 3.5 28.0 - - + +
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Residues in contact with GLY 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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624B GLN 2.9 11.6 + - - -
625B ILE 3.2 3.3 + - - -
627B LEU* 1.3 78.7 - - - +
629B ARG* 1.3 60.1 + - - +
630B THR 3.4 0.3 + - - -
631B VAL* 3.5 14.1 + - - +
632B LYS* 3.6 25.3 - - - +
1003B S9Y 3.7 30.3 - - - -
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Residues in contact with ARG 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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625B ILE* 3.0 38.6 + - - +
626B SER* 3.5 26.9 - - - +
628B GLY* 1.3 77.5 - - - +
630B THR* 1.3 63.4 + - + +
631B VAL 3.5 1.1 + - - -
632B LYS* 4.3 11.2 + - - +
633B ASP* 3.2 29.4 + - - +
730B SER* 6.0 1.6 - - - -
737B ASP 6.1 0.2 - - - -
738B ALA* 5.4 8.9 - - - +
741B 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