Contacts of the helix formed by residues 619 - 625 (chain A) in PDB entry 2Q5H
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 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A LEU* 3.7 22.2 - - + -
573A PHE* 4.0 7.9 - - - -
617A THR* 4.9 9.9 - - + +
618A ILE* 1.3 74.8 - - - +
620A PHE* 1.3 60.0 + - - +
621A ASP* 3.3 7.1 + - - +
622A THR* 2.8 42.5 + - - -
623A VAL* 3.1 6.9 + - - +
631A THR* 4.7 1.4 + - - -
642A ARG* 3.0 35.5 + - - -
672A PHE* 4.9 6.1 - - - -
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Residues in contact with PHE 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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567A LEU* 4.2 25.6 - - + -
568A SER* 4.6 10.3 - - - -
570A ASN* 4.7 9.0 - - + -
573A PHE* 3.8 30.9 - + - -
619A ASP* 1.3 75.3 - - - +
621A ASP* 1.3 56.1 + - - +
623A VAL* 3.1 2.2 + - + +
624A ASN* 2.7 57.4 + - - +
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Residues in contact with ASP 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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619A ASP* 3.2 6.1 + - - +
620A PHE* 1.3 77.1 - - - +
622A THR* 1.3 65.8 + - - +
624A ASN* 4.9 0.7 - - - +
625A LYS* 3.0 68.3 + - + +
627A PRO 4.9 1.6 - - - +
629A THR 5.0 0.9 + - - -
642A ARG* 3.5 19.5 + - - +
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Residues in contact with THR 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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576A PHE* 4.0 4.6 - - + -
618A ILE* 4.0 11.7 - - + -
619A ASP* 2.8 34.1 + - - -
621A ASP* 1.3 77.3 - - - +
623A VAL* 1.3 53.3 + - - +
628A HIS* 2.6 43.8 + - + +
629A THR 2.6 38.3 + - - +
630A ALA* 3.7 8.1 - - + -
642A ARG* 3.6 1.5 + - - +
645A ILE* 4.0 24.7 - - + -
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Residues in contact with VAL 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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570A ASN* 5.9 0.2 - - - +
572A GLU* 3.5 44.4 - - + +
573A PHE* 3.9 36.1 - - + -
576A PHE* 3.6 27.3 - - + -
618A ILE* 4.2 6.5 - - + -
619A ASP 3.1 10.1 + - - +
620A PHE* 3.1 7.6 + - - +
622A THR* 1.3 77.7 - - - +
624A ASN* 1.3 68.2 + - - +
628A HIS* 3.4 15.4 - - - -
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Residues in contact with ASN 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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572A GLU* 4.9 5.2 - - - +
620A PHE* 2.7 52.2 + - - +
621A ASP* 4.9 0.9 - - - +
623A VAL* 1.3 86.4 - - - +
625A LYS* 1.3 68.1 + - + +
626A THR* 3.7 2.6 + - - +
628A HIS* 4.6 3.4 - - - -
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Residues in contact with LYS 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 ASP* 3.0 57.4 + - + +
622A THR 3.7 0.2 - - - +
624A ASN* 1.3 78.7 - - + +
626A THR* 1.3 59.6 + - - +
627A PRO 3.2 11.9 - - - +
628A HIS* 3.1 20.8 + - - -
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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