Contacts of the helix formed by residues 724 - 733 (chain B) in PDB entry 1LD7
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 GLY 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687B PRO 5.8 0.9 - - - -
688B ASP 3.7 4.3 - - - +
689B GLY* 3.6 12.0 - - - -
722B PHE 3.2 1.8 + - - -
723B GLU* 1.3 79.2 + - - +
725B THR* 1.3 63.3 + - - +
727B GLU* 3.2 24.9 + - - +
728B TRP* 3.0 21.3 + - - +
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Residues in contact with THR 725 (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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685B LYS* 3.9 1.6 - - - -
689B GLY* 2.7 26.4 + - - +
691B PHE* 3.6 9.3 - - + -
704B ALA* 4.0 17.5 - - + +
722B PHE* 3.1 38.6 + - + -
723B GLU 3.2 1.2 + - - -
724B GLY* 1.3 74.6 - - - +
726B ALA* 1.3 66.4 + - - +
728B TRP* 3.1 4.1 + - + +
729B ILE* 2.9 41.5 + - + +
758B ALA* 6.1 0.2 - - + -
762B LEU* 4.2 10.1 - - + -
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Residues in contact with ALA 726 (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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722B PHE 4.3 2.8 + - - +
724B GLY 3.4 0.4 - - - -
725B THR* 1.3 77.9 - - - +
727B GLU* 1.3 58.4 + - - +
729B ILE* 3.3 4.0 + - - +
730B ALA* 3.0 28.1 + - - +
759B LEU* 3.6 29.7 - - + +
762B LEU* 4.4 6.3 - - + +
764B ARG* 3.7 43.1 - - + +
767B SER* 4.3 4.8 - - - +
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Residues in contact with GLU 727 (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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724B GLY* 3.2 30.7 + - - +
726B ALA* 1.3 74.3 + - - +
728B TRP* 1.3 66.4 + - - +
730B ALA* 3.3 8.1 + - - +
731B ARG* 3.1 29.3 + - + +
764B ARG* 3.0 34.6 + - - +
767B SER* 5.7 1.6 - - - -
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Residues in contact with TRP 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B ASP* 3.5 47.2 + - - +
689B GLY 4.2 5.2 - - - -
690B SER* 3.5 26.5 - - - -
699B VAL* 4.2 12.3 - - + +
700B ASP* 3.7 8.3 - - - -
701B VAL* 3.6 39.5 - - + -
703B SER* 5.7 0.4 - - - -
704B ALA* 5.1 7.0 - - + -
724B GLY 3.0 8.2 + - - +
725B THR* 3.1 8.0 + - + +
727B GLU* 1.3 76.4 - - - +
729B ILE* 1.3 73.7 + - + +
731B ARG* 3.3 34.9 + - - +
732B CYS* 3.4 25.5 + - - -
741B GLY 3.7 3.6 - - - -
742B VAL* 4.4 4.0 - - + -
743B PRO* 3.8 27.8 - - + +
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Residues in contact with ILE 729 (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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701B VAL* 4.5 7.0 - - + -
704B ALA* 4.1 8.3 - - + -
725B THR* 2.9 35.5 + - + +
726B ALA* 3.6 6.5 - - - +
728B TRP* 1.3 90.2 - - + +
730B ALA* 1.3 56.9 + - - +
732B CYS* 2.7 32.2 + - - +
733B GLN 3.5 2.8 + - - -
739B ILE* 4.5 8.3 - - + +
755B GLY* 3.8 31.9 - - - +
758B ALA* 3.9 28.5 - - + -
759B LEU* 3.8 25.4 - - + +
762B LEU* 5.1 1.1 - - + -
768B LEU* 4.4 1.4 - - - +
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Residues in contact with ALA 730 (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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726B ALA 3.0 13.4 + - - +
727B GLU* 3.3 10.5 + - - +
729B ILE* 1.3 76.0 - - - +
731B ARG* 1.3 63.4 + - + +
733B GLN* 3.0 19.8 + - - +
759B LEU* 5.1 0.2 - - - +
767B SER* 3.5 33.0 - - - +
768B LEU* 3.7 14.3 - - + +
2C FRU 3.6 14.9 - - - +
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Residues in contact with ARG 731 (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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688B ASP* 4.9 10.7 + - - +
727B GLU* 3.1 19.7 + - - +
728B TRP* 3.4 33.8 - - - +
729B ILE 3.1 0.4 - - - -
730B ALA* 1.3 76.8 - - - +
732B CYS* 1.3 60.4 + - - +
733B GLN 3.3 6.6 + - - +
743B PRO* 3.7 40.9 - - + +
744B GLY 4.5 2.6 + - - -
1C GLC 3.6 10.1 + - - -
2C FRU 5.5 0.4 - - - -
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Residues in contact with CYS 732 (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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701B VAL* 3.6 9.2 - - + -
728B TRP* 3.5 47.3 - - - -
729B ILE* 2.7 13.2 + - - +
731B ARG* 1.3 77.3 - - - +
733B GLN* 1.3 62.6 + - - +
734B ASN* 3.5 4.0 + - - +
739B ILE* 3.5 18.4 - - + -
740B GLY* 2.9 29.1 + - - +
742B VAL* 3.9 3.9 - - - +
743B PRO* 3.7 24.4 - - - +
744B GLY 5.4 1.3 + - - -
745B MET 4.7 1.0 - - - +
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Residues in contact with GLN 733 (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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729B ILE 3.5 2.4 + - - -
730B ALA 3.0 12.7 + - - +
731B ARG 3.6 1.2 - - - +
732B CYS* 1.3 78.8 - - - +
734B ASN* 1.3 61.2 + - - +
737B GLY 2.8 21.6 + - - +
738B GLY 3.3 14.6 - - - +
739B ILE* 4.0 7.1 - - + +
768B LEU* 3.6 17.4 - - + -
769B ASN* 2.9 41.1 + - - +
772B SER* 3.4 6.5 + - - -
773B LEU* 3.8 8.1 - - - +
1C GLC 2.7 25.7 + - - -
2C FRU 2.6 41.0 + - - +
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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