Contacts of the helix formed by residues 625 - 637 (chain A) in PDB entry 4Z4Q
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 LYS 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A VAL 4.7 2.1 - - - +
623A GLY 3.4 1.9 - - - +
624A ASP* 1.3 75.7 - - - +
626A VAL* 1.3 64.3 + - - +
628A PRO* 3.5 28.8 - - + +
629A ARG* 3.7 18.4 + - - +
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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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624A ASP 3.4 9.6 + - - +
625A LYS* 1.3 70.8 - - - +
627A GLU* 1.3 61.2 + - - +
629A ARG* 2.8 38.9 + - - +
630A ARG* 2.9 22.5 + - + +
1173A GLY* 3.9 33.7 - - - +
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Residues in contact with GLU 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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625A LYS* 4.8 0.2 - - - +
626A VAL* 1.3 78.5 - - - +
628A PRO* 1.3 68.8 - - + +
630A ARG* 3.4 23.5 + - - +
631A LYS* 3.1 24.6 + - - +
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Residues in contact with PRO 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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620A VAL* 3.8 24.2 - - + +
625A LYS* 3.5 30.7 - - + +
626A VAL 3.4 3.6 - - - -
627A GLU* 1.3 95.1 - - + +
629A ARG* 1.3 55.7 + - - +
631A LYS* 3.9 5.8 - - + +
632A TRP* 3.0 26.9 + - - +
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Residues in contact with ARG 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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464A LYS* 3.8 18.1 - - - +
620A VAL 3.8 14.4 + - - +
621A LEU* 3.3 21.0 + - + +
622A MET 3.7 3.8 - - - -
623A GLY 2.2 48.5 + - - +
624A ASP 4.8 0.8 + - - -
625A LYS 3.7 8.9 + - - +
626A VAL* 2.8 44.7 + - + +
628A PRO* 1.3 71.9 - - - +
630A ARG* 1.3 65.0 + - - +
632A TRP* 3.0 7.1 + - - +
633A ILE* 2.9 40.6 + - + +
1017A PHE* 4.2 20.4 - - + -
1172A ALA* 5.1 1.1 - - - -
1173A GLY* 4.3 16.7 - - - +
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Residues in contact with ARG 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 VAL* 2.9 20.0 + - - +
627A GLU* 3.6 25.3 - - - +
629A ARG* 1.3 76.2 - - - +
631A LYS* 1.3 56.4 + - - +
633A ILE* 3.1 7.8 + - - +
634A GLU* 2.9 51.9 + - - +
1173A GLY* 3.4 33.2 + - - +
1174A TYR* 3.8 24.6 + - + -
1233A LYS* 5.2 9.9 - - - +
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Residues in contact with LYS 631 (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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627A GLU 3.1 14.5 + - - +
628A PRO* 3.9 7.2 - - + +
630A ARG* 1.3 74.6 - - - +
632A TRP* 1.3 67.6 + - - +
634A GLU* 3.2 13.2 + - - +
635A ASP* 3.0 57.3 + - - +
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Residues in contact with TRP 632 (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 ARG* 3.2 45.0 - - - +
620A VAL* 4.0 20.6 - - + -
621A LEU* 3.5 32.9 - - + +
628A PRO 3.0 19.7 + - - +
629A ARG* 3.0 7.2 + - - +
631A LYS* 1.3 77.3 - - - +
633A ILE* 1.3 69.2 + - + +
635A ASP* 3.8 2.4 - - - -
636A ASN* 2.9 70.3 + - + +
637A VAL* 4.6 7.0 - - + -
1014A GLY* 4.0 22.7 - - - -
1017A PHE* 4.8 2.5 - + - -
1018A GLY* 4.5 18.2 - - - -
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Residues in contact with ILE 633 (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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629A ARG* 2.9 35.6 + - + +
630A ARG* 3.5 7.2 - - - +
632A TRP* 1.3 90.6 - - + +
634A GLU* 1.3 61.0 + - - +
637A VAL* 2.9 49.1 + - + +
639A PHE* 3.9 19.6 - - + -
1017A PHE* 4.6 5.2 - - + -
1021A SER* 4.2 21.1 - - - -
1025A ILE* 4.1 9.0 - - + -
1172A ALA 3.7 25.1 - - - +
1173A GLY* 4.4 2.9 - - - -
1174A TYR* 4.9 7.2 - - + -
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Residues in contact with GLU 634 (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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630A ARG* 2.9 46.2 + - - +
631A LYS* 3.2 12.5 + - - +
633A ILE* 1.3 77.5 - - + +
635A ASP* 1.3 68.0 + - - +
636A ASN 3.6 0.2 + - - -
637A VAL 4.3 7.3 - - - +
639A PHE* 5.3 6.3 - - + -
1174A TYR* 3.5 18.4 + - - +
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Residues in contact with ASP 635 (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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631A LYS* 3.0 41.1 + - - +
632A TRP* 4.0 4.5 - - - +
634A GLU* 1.3 84.5 - - - +
636A ASN* 1.3 67.9 + - - +
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Residues in contact with ASN 636 (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 ARG* 4.8 2.7 - - - +
632A TRP* 2.9 70.2 + - + +
635A ASP* 1.3 89.1 - - - +
637A VAL* 1.3 65.9 + - + +
638A LYS* 3.1 7.4 + - - +
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Residues in contact with VAL 637 (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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632A TRP* 4.6 5.6 - - + -
633A ILE* 2.9 41.2 + - + +
634A GLU 4.3 6.1 - - - +
636A ASN* 1.3 71.6 - - - +
638A LYS* 1.3 59.7 + - - +
639A PHE* 3.3 49.2 + - + -
1018A GLY* 4.0 31.6 - - - +
1021A SER* 4.4 5.6 - - - -
1022A LYS* 3.9 17.7 - - + -
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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