Contacts of the helix formed by residues 616 - 625 (chain A) in PDB entry 7ACN
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 VAL 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A LEU* 3.8 28.8 - - + +
559A ILE* 4.5 10.8 - - + -
590A LEU* 3.6 17.7 - - + +
591A LEU* 3.9 23.3 - - + +
603A ASN* 2.8 32.5 + - - +
604A SER 4.4 0.2 - - - +
605A VAL* 4.0 29.2 - - + -
615A PRO* 1.3 72.0 - - - +
617A PRO* 1.4 59.6 - - + +
619A THR* 3.1 3.1 + - - -
620A ALA* 2.9 27.5 + - - +
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Residues in contact with PRO 617 (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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587A SER 3.7 16.6 - - - +
588A ASN* 3.3 35.9 - - + +
590A LEU* 3.6 15.9 - - + +
592A ILE* 3.7 7.6 - - + -
603A ASN* 3.6 9.4 - - - +
615A PRO* 3.6 6.3 - - + -
616A VAL* 1.4 94.1 - - + +
618A ASP* 1.3 61.9 + - - +
620A ALA* 3.3 3.8 + - + +
621A ARG* 2.9 35.8 + - - +
654A LEU* 3.9 10.8 - - + +
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Residues in contact with ASP 618 (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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588A ASN* 5.7 0.9 - - - +
615A PRO* 3.5 35.4 + - + +
616A VAL 3.3 0.4 - - - -
617A PRO* 1.3 78.9 - - - +
619A THR* 1.3 62.4 + - - +
621A ARG* 3.4 9.7 + - - +
622A TYR* 2.9 27.9 + - - +
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Residues in contact with THR 619 (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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558A LEU* 4.1 6.3 - - + +
605A VAL* 3.8 20.7 + - + +
606A ARG 4.5 0.7 - - - +
607A ASN* 4.0 25.8 + - + +
614A GLY* 4.1 7.8 + - - -
615A PRO 2.6 25.6 + - - -
616A VAL 3.6 3.6 - - - -
618A ASP* 1.3 75.2 - - - +
620A ALA* 1.3 64.3 + - - +
622A TYR* 3.2 7.0 + - - +
623A TYR* 3.0 54.3 + - + +
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Residues in contact with ALA 620 (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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558A LEU* 3.8 16.2 - - + +
590A LEU* 4.6 1.8 - - + -
616A VAL 2.9 13.7 + - - +
617A PRO* 3.6 7.6 - - + +
619A THR* 1.3 75.1 - - - +
621A ARG* 1.3 58.5 + - - +
623A TYR* 3.3 3.8 + - - +
624A LYS* 2.9 29.3 + - - +
630A TRP* 3.8 33.2 - - + +
654A LEU* 3.5 19.7 - - + +
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Residues in contact with ARG 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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584A ASP* 2.8 53.0 + - - -
587A SER* 4.0 8.7 - - - -
588A ASN* 2.7 33.1 + - - +
617A PRO 2.9 22.6 + - - +
618A ASP* 3.7 8.1 - - - +
619A THR 3.3 0.2 - - - -
620A ALA* 1.3 74.8 - - - +
622A TYR* 1.3 58.5 + - - +
624A LYS* 3.1 9.5 + - + +
625A GLN* 2.8 32.4 + - - +
653A HIS* 4.4 0.8 - - - -
654A LEU* 3.7 28.0 - - + +
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Residues in contact with TYR 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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607A ASN* 3.4 26.2 - - - +
609A VAL* 3.4 39.6 - - + +
610A THR* 3.9 19.5 - - + +
618A ASP 2.9 15.3 + - - +
619A THR* 3.2 7.8 + - - +
621A ARG* 1.3 76.2 - - - +
623A TYR* 1.3 71.4 + + - +
625A GLN* 4.1 10.5 - - - -
626A HIS* 2.7 67.5 + + + -
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Residues in contact with TYR 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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556A GLN* 3.7 33.4 + - + -
557A ILE 4.8 0.9 + - - -
558A LEU* 3.9 20.3 + - + -
606A ARG 3.5 11.1 + - - -
607A ASN* 3.7 18.7 - - - -
608A ALA* 3.2 26.0 + - + -
609A VAL* 4.8 0.7 - - + -
619A THR* 3.0 35.9 + - + +
620A ALA 3.8 4.3 - - - +
622A TYR* 1.3 79.5 - + - +
624A LYS* 1.3 63.6 + - - +
626A HIS 3.1 2.8 + - - -
627A GLY 3.0 5.0 + - - -
628A ILE* 2.8 68.1 + - + +
630A TRP* 4.0 19.1 - + + -
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Residues in contact with LYS 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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620A ALA 2.9 17.4 + - - +
621A ARG* 3.5 8.2 - - + +
623A TYR* 1.3 76.8 - - - +
625A GLN* 1.3 61.2 + - - +
627A GLY* 3.2 12.2 + - - -
628A ILE 4.2 4.7 + - - +
653A HIS* 2.6 47.6 + - - +
654A LEU* 3.6 24.8 + - + +
655A GLY* 4.2 9.0 - - - +
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Residues in contact with GLN 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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621A ARG 2.8 20.8 + - - +
622A TYR* 3.4 13.0 - - - +
624A LYS* 1.3 73.5 - - - +
626A HIS* 1.3 91.6 + - - +
627A GLY 3.5 0.3 + - - -
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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