Contacts of the helix formed by residues 625 - 637 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619B ASN 5.5 0.3 - - - +
620B VAL 4.6 3.1 - - - +
623B GLY* 3.3 1.9 - - - -
624B ASP* 1.3 83.6 - - - +
626B VAL* 1.3 63.0 + - - +
627B GLU 3.7 0.2 - - - -
628B PRO* 3.7 25.9 - - + +
629B ARG* 3.5 17.3 + - - +
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Residues in contact with VAL 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B ASP 4.0 9.9 - - - +
625B LYS* 1.3 72.1 - - - +
627B GLU* 1.3 67.6 + - - +
629B ARG* 3.3 21.7 + - - +
630B ARG* 3.0 21.2 + - + +
1173B GLY* 4.4 24.9 - - - +
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Residues in contact with GLU 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B LYS* 4.9 0.2 - - - +
626B VAL* 1.3 79.1 - - - +
628B PRO* 1.3 74.9 - - + +
630B ARG* 3.1 9.3 + - - +
631B LYS* 3.0 18.2 + - - +
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Residues in contact with PRO 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B VAL* 4.9 17.9 - - + -
625B LYS* 3.7 26.7 - - + +
626B VAL 3.5 3.6 - - - -
627B GLU* 1.3 92.9 - - + +
629B ARG* 1.3 49.9 + - - +
631B LYS* 2.8 13.1 + - + +
632B TRP* 2.8 33.4 + - - +
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Residues in contact with ARG 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LYS* 3.7 20.2 - - - +
620B VAL 3.6 15.6 + - - +
621B LEU* 3.0 24.7 + - + +
623B GLY 2.3 43.4 + - - +
624B ASP 4.3 0.6 + - - -
625B LYS 3.5 14.0 + - - +
626B VAL* 3.3 30.2 + - - +
628B PRO* 1.3 74.4 - - - +
630B ARG* 1.3 66.3 + - - +
632B TRP* 3.3 8.2 + - - +
633B ILE* 3.0 43.9 + - + +
1017B PHE* 4.1 17.0 - - + -
1172B ALA* 5.1 1.3 - - - +
1173B GLY* 4.5 16.0 - - - +
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Residues in contact with ARG 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B VAL* 3.0 13.9 + - + +
627B GLU* 3.1 13.0 + - - +
629B ARG* 1.3 73.6 - - - +
631B LYS* 1.3 58.3 + - - +
633B ILE* 3.1 7.0 + - - +
634B GLU* 2.9 51.4 + - - +
1173B GLY* 3.5 32.2 - - - +
1174B TYR* 3.7 21.7 + - + +
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Residues in contact with LYS 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627B GLU 3.0 9.6 + - - +
628B PRO* 2.8 17.4 + - + +
630B ARG* 1.3 69.4 - - - +
632B TRP* 1.3 64.3 + - - +
634B GLU* 3.3 12.9 + - - +
635B ASP* 3.0 36.7 + - - +
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Residues in contact with TRP 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B ARG* 3.8 39.8 - - - +
620B VAL* 4.5 18.6 - - + -
621B LEU* 3.5 31.2 - - + -
628B PRO 2.8 15.8 + - - +
629B ARG* 3.3 11.9 + - - +
631B LYS* 1.3 71.7 - - - +
633B ILE* 1.3 69.4 + - + +
635B ASP* 3.8 4.2 - - - -
636B ASN* 2.8 71.4 + - + +
637B VAL* 4.6 12.3 - - + -
1014B GLY* 3.8 24.5 - - - -
1017B PHE* 4.9 2.2 - + - -
1018B GLY* 4.7 9.2 - - - -
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Residues in contact with ILE 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B ARG* 3.0 41.9 + - + +
630B ARG* 3.6 4.7 - - - +
632B TRP* 1.3 90.3 - - + +
634B GLU* 1.3 65.2 + - - +
637B VAL* 3.1 46.8 + - + +
639B PHE* 4.1 17.7 - - + -
1017B PHE* 4.5 5.6 - - + -
1021B SER* 4.3 18.8 - - - -
1025B ILE* 4.1 10.3 - - + -
1172B ALA 3.9 24.5 - - - +
1173B GLY* 4.3 3.1 - - - -
1174B TYR* 5.1 5.8 - - + -
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Residues in contact with GLU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ARG* 2.9 33.3 + - - +
631B LYS* 3.7 11.6 - - - +
633B ILE* 1.3 77.8 - - - +
635B ASP* 1.3 63.4 + - - +
637B VAL 4.7 5.2 - - - +
639B PHE* 5.4 6.4 - - + -
1174B TYR* 3.0 29.5 + - - +
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Residues in contact with ASP 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B LYS* 3.0 28.2 + - - +
632B TRP* 3.9 5.8 - - - +
634B GLU* 1.3 84.2 - - - +
636B ASN* 1.3 68.4 + - - +
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Residues in contact with ASN 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B ARG* 5.6 1.4 - - - +
632B TRP* 2.8 72.1 + - + +
635B ASP* 1.3 89.3 - - - +
637B VAL* 1.3 66.5 + - - +
638B LYS* 3.3 6.9 + - - +
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Residues in contact with VAL 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B TRP* 4.6 11.7 - - + -
633B ILE* 3.1 41.8 + - + +
634B GLU 4.7 5.2 - - - +
635B ASP 5.4 0.2 - - - -
636B ASN* 1.3 73.2 - - - +
638B LYS* 1.3 61.2 + - - +
639B PHE* 3.4 36.4 + - + -
1018B GLY* 4.3 17.7 - - - +
1021B SER* 4.6 3.6 - - - -
1022B LYS* 3.7 34.8 - - + -
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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