Contacts of the helix formed by residues 621 - 630 (chain A) in PDB entry 4YOC
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 THR 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A THR* 1.3 97.2 + - - +
622A LYS* 1.3 60.1 + - - +
623A LEU* 4.2 1.6 - - - -
624A VAL* 3.2 21.5 + - - +
625A TYR* 2.9 17.8 + - - +
848A GLY* 4.2 23.6 - - - +
1195A LEU* 5.9 0.4 - - + -
1199A MET* 4.5 13.5 - - + -
1253A SER* 3.9 22.8 + - - +
1256A ASP* 2.8 28.6 + - - +
1257A TYR* 4.4 9.6 - - + +
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Residues in contact with LYS 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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620A THR 4.2 0.2 + - - -
621A THR* 1.3 73.7 - - - +
623A LEU* 1.3 57.3 + - - +
625A TYR* 3.9 7.9 - - - +
626A GLN* 2.9 44.2 + - - +
848A GLY* 5.1 11.9 + - - +
849A MET 5.1 1.3 - - - +
850A ASP* 3.6 38.0 + - + +
851A PRO* 4.2 13.9 - - + -
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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
----------------------------------------------------------
621A THR* 3.1 0.6 - - - -
622A LYS* 1.3 77.5 - - - +
624A VAL* 1.3 67.3 + - + +
626A GLN* 3.2 8.1 + - - +
627A ILE* 2.9 30.2 + - + +
846A GLU 6.1 0.2 - - - +
849A MET 5.2 9.4 + - - +
851A PRO* 4.8 10.2 - - + +
1256A ASP* 3.5 30.1 - - - +
1259A ARG* 4.6 6.3 - - - +
1286A CYS* 4.4 4.7 - - - -
1289A ARG* 3.5 63.0 + - + +
1290A MET* 4.0 21.1 - - + -
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Residues in contact with VAL 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A THR* 4.0 2.9 - - - +
621A THR* 3.2 21.6 + - - +
623A LEU* 1.3 78.3 - - + +
625A TYR* 1.3 64.4 + - - +
627A ILE* 3.0 2.9 + - - +
628A PHE* 2.9 53.5 + - + -
1249A VAL* 3.7 22.9 - - + +
1252A LEU* 4.1 8.3 - - + +
1253A SER* 4.0 9.0 - - - +
1256A ASP* 4.1 5.4 - - + -
1286A CYS* 3.5 26.0 - - - -
1290A MET* 4.1 13.9 - - + -
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Residues in contact with TYR 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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617A LYS* 6.4 2.5 - - + -
620A THR* 3.4 27.2 + - + +
621A THR 2.9 20.0 + - - +
622A LYS* 3.9 7.6 - - - +
624A VAL* 1.3 77.1 - - - +
626A GLN* 1.3 65.7 + - + +
628A PHE* 3.4 5.6 + - + +
629A ASP* 2.9 56.6 + - - +
1244A LYS* 4.3 23.0 + - + -
1249A VAL* 6.0 1.6 - - - -
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Residues in contact with GLN 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 LYS* 2.9 30.6 + - + +
623A LEU* 3.4 5.5 - - - +
625A TYR* 1.3 80.0 - - + +
627A ILE* 1.3 59.4 + - + +
629A ASP* 4.3 4.7 - - - -
630A THR* 2.3 47.9 + - - +
851A PRO* 3.2 40.6 - - - +
1289A ARG* 5.3 1.6 + - - -
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Residues in contact with ILE 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 20.0 + - - +
624A VAL* 3.0 11.4 + - - +
626A GLN* 1.3 78.8 - - + +
628A PHE* 1.3 70.9 + - + +
629A ASP 3.5 0.2 + - - -
630A THR* 4.4 2.6 - - - -
631A PHE* 3.5 19.8 + - - +
1282A LEU* 4.6 11.8 - - + +
1285A ARG* 4.0 36.8 - - + +
1286A CYS* 4.3 19.7 - - + +
1289A ARG* 3.9 36.3 - - + +
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Residues in contact with PHE 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 VAL* 2.9 50.4 + - + +
625A TYR* 3.7 4.5 - - + +
627A ILE* 1.3 80.0 - - + +
629A ASP* 1.3 58.7 + - - +
631A PHE* 4.2 1.6 + - - -
632A PHE* 5.0 0.2 - - - -
1240A TYR* 2.4 41.8 + + - +
1243A PHE* 3.4 38.6 - + - -
1244A LYS* 3.4 26.4 + - + +
1248A VAL* 6.0 0.2 - - + -
1249A VAL* 3.9 25.4 - - + -
1252A LEU* 4.0 19.1 - - + -
1282A LEU* 3.9 26.7 - - + -
1283A THR 4.9 0.2 - - - -
1286A CYS* 4.1 12.8 - - - -
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Residues in contact with ASP 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 TYR* 2.9 43.0 + - + +
626A GLN* 3.9 4.0 - - - +
628A PHE* 1.3 79.1 - - - +
630A THR* 1.3 58.5 + - - +
631A PHE 3.0 8.6 + - - -
632A PHE* 3.4 23.8 + - - +
1244A LYS* 3.0 21.0 + - - +
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Residues in contact with THR 630 (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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626A GLN* 2.3 40.5 + - - +
627A ILE* 4.4 2.9 - - - -
629A ASP* 1.3 71.9 - - - +
631A PHE* 1.3 58.9 + - - +
632A PHE 3.4 0.8 + - - -
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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