Contacts of the helix formed by residues 625 - 634 (chain B) in PDB entry 3U44
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 SER 625 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LYS* 4.3 27.6 - - - -
161B LYS* 4.5 2.6 - - - +
620B GLU* 5.2 10.3 - - - -
623B VAL 4.0 2.0 + - - -
624B LEU* 1.3 75.4 - - - +
626B ASP* 1.3 65.6 + - - +
627B ASP* 3.1 13.0 + - - +
628B ASP* 2.5 47.5 + - - -
629B ARG* 3.0 14.7 + - - +
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Residues in contact with ASP 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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103A ARG* 3.0 25.7 + - - +
618B PRO* 5.7 1.0 - - - +
620B GLU* 5.3 6.0 + - - +
624B LEU 4.0 0.2 + - - -
625B SER* 1.3 72.7 - - - +
627B ASP* 1.3 64.7 + - - +
629B ARG* 3.6 8.7 + - - +
630B GLU* 2.9 42.3 + - - +
641B SER 5.7 0.2 - - - +
643B GLY* 3.0 22.7 + - - -
644B ARG* 2.7 25.2 + - - +
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Residues in contact with ASP 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 5.5 2.5 + - - -
119A LYS* 3.9 17.2 + - - +
396A PHE* 3.9 22.8 - - + -
400A GLN* 4.9 5.6 + - - -
625B SER* 3.0 8.5 + - - +
626B ASP* 1.3 79.6 - - - +
628B ASP* 1.3 66.3 + - - +
630B GLU* 3.3 14.4 + - - +
631B TRP* 3.0 23.4 + - - +
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Residues in contact with ASP 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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154B GLY 3.9 6.1 - - - +
158B LEU* 3.0 44.7 - - + +
161B LYS* 3.7 16.5 + - - -
624B LEU* 4.4 12.1 - - + -
625B SER* 2.5 45.0 + - - +
627B ASP* 1.3 75.0 - - - +
629B ARG* 1.3 63.7 + - - +
631B TRP* 2.9 8.5 + - - +
632B LEU* 2.9 26.5 + - - +
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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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126B MET* 4.3 12.1 - - - -
129B GLU* 2.7 42.4 + - - -
621B ASN 5.9 0.2 + - - -
622B GLY* 5.8 5.1 - - - -
623B VAL 5.8 0.2 - - - +
624B LEU* 3.7 32.6 + - + +
625B SER 3.0 19.0 + - - +
626B ASP* 3.9 7.9 - - - +
628B ASP* 1.3 76.3 - - - +
630B GLU* 1.3 64.3 + - + +
631B TRP 3.2 0.2 + - - -
632B LEU* 3.2 12.7 + - - +
633B LYS* 3.1 27.2 + - + +
637B VAL 5.2 0.2 - - - +
639B LEU* 3.8 14.7 - - + +
640B SER* 2.7 30.8 + - - +
641B SER 3.5 20.6 - - - +
642B GLY* 5.0 7.8 - - - -
643B GLY 5.0 1.1 - - - +
645B GLU* 5.8 2.2 - - - +
646B ARG* 6.1 0.8 - - - +
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Residues in contact with GLU 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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103A ARG* 3.2 24.7 + - - -
626B ASP* 2.9 41.0 + - - +
627B ASP* 3.7 11.8 - - - +
629B ARG* 1.3 78.0 - - + +
631B TRP* 1.3 61.2 + - - +
633B LYS* 3.4 32.4 - - + +
634B THR* 3.8 10.0 - - - +
644B ARG* 3.7 25.4 + - - +
645B GLU* 5.3 8.0 - - + +
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Residues in contact with TRP 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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143B MET 6.1 0.9 - - - -
146B SER* 5.5 0.9 - - - -
147B GLY* 4.8 15.5 - - - -
155B GLU* 3.1 49.1 + - + -
158B LEU* 3.7 24.9 - - + -
627B ASP 3.0 11.8 + - - +
628B ASP* 2.9 11.8 + - - +
630B GLU* 1.3 73.3 - - - +
632B LEU* 1.3 91.2 + - + +
633B LYS 3.0 1.8 - - - -
634B THR* 2.6 45.4 + - - -
635B ILE* 3.4 36.0 + - + +
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Residues in contact with LEU 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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143B MET* 4.0 27.6 - - + -
158B LEU* 4.1 14.6 - - + -
162B LEU* 4.6 4.5 - - + -
624B LEU* 3.8 28.9 - - + -
628B ASP 2.9 18.4 + - - +
629B ARG* 3.2 12.3 + - - +
631B TRP* 1.3 104.0 - - + +
633B LYS* 1.3 62.4 + - - +
635B ILE* 2.8 18.9 + - + +
637B VAL* 3.3 26.3 + - + +
639B LEU* 4.3 15.0 - - + -
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Residues in contact with LYS 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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248B GLU* 5.7 1.2 + - - -
629B ARG 3.1 12.1 - - - +
630B GLU* 3.4 31.8 - - + +
631B TRP 3.0 0.2 + - - -
632B LEU* 1.3 77.9 - - - +
634B THR* 1.3 59.4 + - + +
635B ILE 3.1 4.9 + - - -
636B GLY* 3.2 14.4 + - - -
637B VAL 3.2 14.4 + - - +
638B GLU* 5.5 4.0 - - - -
639B LEU 5.7 2.5 - - - +
644B ARG* 5.2 8.5 - - - +
645B GLU* 4.1 32.4 + - - +
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Residues in contact with THR 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 GLU 3.8 11.7 - - - +
631B TRP* 2.6 35.5 + - - +
633B LYS* 1.3 72.8 - - + +
635B ILE* 1.3 64.0 + - - +
636B GLY 3.3 2.0 - - - -
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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