Contacts of the helix formed by residues 622 - 628 (chain A) in PDB entry 2HWK
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 622 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A SER* 3.6 18.8 - - - -
621A ASP* 1.3 77.9 + - - +
623A SER* 1.3 68.3 + - - +
624A SER 3.2 2.5 - - - -
625A PHE* 3.2 11.3 + - + +
626A VAL* 3.0 22.5 + - + +
641A LEU* 4.2 8.7 - - + +
678A PHE* 3.7 35.9 - + + -
680A ASN* 4.4 0.7 - - - -
682A ARG* 3.9 19.3 - - - -
720A ILE* 4.0 13.7 - - + -
748A PRO* 3.4 34.8 - - + -
750A SER* 4.8 1.6 - - - -
751A SER* 4.1 8.7 - - - -
756A GLU* 3.3 26.5 - - + -
758A LEU* 3.9 25.8 - - + -
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Residues in contact with SER 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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621A ASP* 3.0 25.5 + - - -
622A PHE* 1.3 77.7 - - - +
624A SER* 1.3 61.9 + - - +
626A VAL* 3.3 3.0 + - - +
627A SER* 3.0 28.5 + - - -
641A LEU* 3.5 16.6 - - - +
642A SER* 3.2 28.1 + - - -
643A VAL* 4.5 2.6 - - - +
644A PRO* 5.2 2.9 - - - -
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Residues in contact with SER 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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621A ASP* 4.5 10.3 + - - -
623A SER* 1.3 79.4 - - - +
625A PHE* 1.3 63.8 + - - +
627A SER* 3.4 8.7 + - - -
628A LYS* 3.0 49.7 + - - +
750A SER* 5.6 3.6 - - - -
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Residues in contact with PHE 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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622A PHE* 3.2 19.9 + - + +
624A SER* 1.3 84.0 + - - +
626A VAL* 1.3 70.1 + - + +
628A LYS* 3.4 20.1 + - + +
629A LEU* 3.5 29.3 + - + +
678A PHE* 5.9 0.2 - + - -
718A VAL* 4.3 9.0 - - + -
746A CYS* 4.3 20.9 - - + -
748A PRO* 3.9 24.9 - - + -
758A LEU* 3.5 28.5 - - + -
760A VAL* 4.0 24.9 - - + -
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Residues in contact with VAL 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 PHE* 3.0 19.5 + - + +
623A SER 3.8 3.4 - - - +
625A PHE* 1.3 75.7 - - + +
627A SER* 1.3 63.8 + - - +
628A LYS 3.1 1.8 - - - -
629A LEU* 3.0 32.1 + - + +
634A VAL* 4.2 20.9 - - + -
641A LEU* 4.0 17.0 - - + -
643A VAL* 3.8 27.4 - - + -
646A LYS* 3.3 10.4 - - - -
676A ILE* 4.5 6.5 - - + -
678A PHE* 4.0 26.0 - - + -
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Residues in contact with SER 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 SER 3.0 16.0 + - - -
624A SER* 3.5 12.8 - - - -
626A VAL* 1.3 75.8 - - - +
628A LYS* 1.3 61.7 + - - +
629A LEU 3.8 0.9 - - - +
643A VAL* 3.8 18.5 - - - +
644A PRO* 3.8 26.5 + - - +
646A LYS* 3.2 20.2 + - - +
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Residues in contact with LYS 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 SER* 3.0 39.3 + - - +
625A PHE* 3.7 11.6 - - + +
626A VAL 3.1 0.8 - - - -
627A SER* 1.3 77.9 - - - +
629A LEU* 1.3 61.2 + - - +
630A LYS* 3.8 3.5 + - - +
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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