Contacts of the helix formed by residues 620 - 630 (chain A) in PDB entry 3KSY
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 ASP 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A ILE* 3.9 19.3 - - - +
599A PRO 3.6 16.1 - - - +
612A ARG 5.2 9.1 + - - +
613A LEU 5.9 0.8 + - - -
618A TYR* 3.1 34.7 + - - -
619A ALA* 1.3 80.3 - - - +
621A PRO* 1.3 66.4 - - + +
622A ASN* 4.8 0.9 - - + +
623A PHE* 3.9 24.0 - - + +
624A VAL* 3.0 29.9 + - - +
688A ARG* 5.4 0.8 - - - +
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Residues in contact with PRO 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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272A GLU* 5.7 2.5 - - - +
619A ALA* 3.6 9.9 - - + +
620A ASP* 1.3 82.9 - - + +
622A ASN* 1.3 76.5 + - + +
624A VAL* 3.2 8.1 + - + +
625A ARG* 3.1 29.5 + - - +
691A ASN* 6.4 0.2 - - - +
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Residues in contact with ASN 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 ASP* 3.5 1.1 - - + -
621A PRO* 1.3 82.1 - - + +
623A PHE* 1.3 62.0 + - - +
625A ARG* 3.3 32.7 + - - +
626A THR* 3.0 28.9 + - - +
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Residues in contact with PHE 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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600A ILE* 6.1 4.0 - - + -
601A ILE* 3.2 37.2 - - + -
609A LEU* 3.6 17.5 - - + -
612A ARG* 4.1 7.6 - - + -
613A LEU* 3.4 46.4 - - + -
620A ASP* 3.9 23.3 + - + +
621A PRO 3.3 0.4 - - - -
622A ASN* 1.3 79.2 - - - +
624A VAL* 1.3 59.0 + - + +
626A THR* 4.0 4.0 - - - -
627A PHE* 2.9 49.8 + + - +
958A PHE* 3.7 27.1 - + - -
962A ARG* 6.2 0.7 - - - -
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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
----------------------------------------------------------
613A LEU* 3.6 29.4 - - + +
620A ASP 3.0 19.1 - - - +
621A PRO* 3.2 9.2 + - + +
623A PHE* 1.3 77.8 - - + +
625A ARG* 1.3 61.6 + - - +
627A PHE* 4.0 0.9 - - - +
628A LEU* 3.2 32.6 + - + +
688A ARG* 6.5 0.4 - - + -
691A ASN* 5.0 9.6 - - - +
692A VAL* 3.6 37.5 - - + +
695A HIS* 4.4 16.4 - - + +
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Residues in contact with ARG 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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272A GLU* 3.3 27.5 + - - -
621A PRO* 3.1 14.8 + - - +
622A ASN* 3.3 49.5 + - - +
624A VAL* 1.3 74.3 - - - +
626A THR* 1.3 69.5 + - - +
628A LEU* 3.1 15.3 + - - +
629A THR* 3.2 22.1 + - - +
695A HIS* 6.5 1.3 - - - -
972A GLN* 6.2 0.7 - - - -
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Residues in contact with THR 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 ASN* 3.0 15.1 + - - +
623A PHE* 4.0 4.5 - - - -
625A ARG* 1.3 82.2 + - - +
627A PHE* 1.3 63.4 + - - +
629A THR* 2.9 17.8 + - - -
630A THR* 3.0 24.1 + - - +
958A PHE* 3.7 26.0 - - + -
961A ARG 4.1 2.5 - - - +
962A ARG* 3.9 26.6 - - + +
965A ALA* 4.2 13.6 - - + +
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Residues in contact with PHE 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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606A VAL* 5.7 2.7 - - + -
609A LEU* 4.3 18.4 - - + -
610A ILE* 4.6 7.4 - - + -
613A LEU* 3.7 33.9 - - + -
623A PHE* 2.9 37.0 + + + +
624A VAL 4.0 2.9 - - - +
626A THR* 1.3 73.4 - - - +
628A LEU* 1.3 70.6 + - + +
630A THR* 4.5 0.4 - - - -
631A TYR* 3.0 49.6 + - + +
634A PHE* 4.2 19.5 - + - -
635A CYS* 5.8 2.2 - - - -
640A LEU* 3.8 34.5 - - + -
958A PHE* 3.9 28.5 - + + -
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Residues in contact with LEU 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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613A LEU* 5.6 0.4 - - + -
624A VAL* 3.2 27.2 + - + +
625A ARG* 3.1 7.8 + - - +
627A PHE* 1.3 92.4 - - + +
629A THR* 1.3 57.3 + - - +
631A TYR* 3.2 19.2 - - + -
632A ARG* 3.4 4.2 + - - -
640A LEU* 4.5 17.5 - - + -
692A VAL* 3.7 23.1 - - + +
695A HIS* 3.6 28.5 - - + -
696A TRP* 4.0 10.8 - - + +
700A HIS* 2.8 49.1 - - + +
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Residues in contact with THR 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 ARG* 3.2 17.5 + - - +
626A THR* 2.9 11.7 + - - -
628A LEU* 1.3 82.0 - - - +
630A THR* 1.3 69.4 + - + +
631A TYR 3.7 1.1 - - - -
632A ARG* 3.6 14.5 + - - +
700A HIS* 5.0 1.9 - - - -
801A PRO* 3.8 35.7 - - + +
802A SER* 4.0 8.0 - - - +
805A VAL* 3.8 10.8 - - + +
965A ALA* 5.2 5.2 - - + -
968A THR* 4.7 7.4 - - + +
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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
----------------------------------------------------------
626A THR* 3.0 16.4 + - - +
627A PHE* 3.6 2.6 + - - -
629A THR* 1.3 92.4 - - + +
631A TYR* 1.3 57.0 + - - +
632A ARG 3.5 1.8 - - - +
633A SER* 3.4 10.5 + - - -
634A PHE* 3.4 16.1 - - - -
805A VAL* 3.7 33.9 - - + -
958A PHE* 4.5 2.4 - - - -
961A ARG* 3.0 45.8 + - - +
964A VAL* 4.8 1.1 - - + -
965A ALA* 4.6 9.2 - - + +
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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