Contacts of the strand formed by residues 753 - 759 (chain B) in PDB entry 1DDJ
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 TYR 753 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549B GLY* 2.7 32.2 + - - -
551B PRO* 3.9 9.2 - - + -
555B PRO* 3.5 34.1 - - + +
557B LYS* 4.0 17.5 - - - +
573B TRP* 3.7 20.2 - + - -
575B TRP* 3.5 32.5 - + + -
665B ALA* 4.9 1.4 - - - +
666B CYS* 3.8 8.8 + - - -
681B PHE* 4.1 13.6 - + - -
746B VAL* 3.8 21.5 - - + -
747B CYS 3.9 1.6 - - - -
748B PHE* 3.6 46.8 - + + +
752B LYS* 1.3 73.7 - - - +
754B ILE* 1.3 62.7 + - - +
755B LEU 4.3 0.2 + - - -
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Residues in contact with ILE 754 (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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666B CYS* 3.6 20.0 - - + +
667B LEU 3.9 3.8 - - - +
668B PRO* 3.7 26.0 - - + -
746B VAL* 3.3 2.9 - - - -
747B CYS 2.9 34.4 + - - +
749B GLU* 3.2 41.5 - - + +
752B LYS* 4.2 23.8 - - + +
753B TYR* 1.3 79.0 - - - +
755B LEU* 1.3 61.8 + - - +
756B GLN* 3.1 29.1 + - - +
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Residues in contact with LEU 755 (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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591B THR* 3.8 23.6 - - + +
593B ILE* 4.3 3.4 - - + -
599B LEU* 3.7 30.5 - - + -
665B ALA* 4.3 9.8 - - + +
666B CYS 2.9 19.7 + - - +
667B LEU* 4.2 13.2 - - + -
668B PRO* 3.2 24.3 - - - +
744B PRO* 3.6 24.5 - - + -
745B LEU 3.5 9.2 - - - +
746B VAL* 3.9 7.7 - - + +
753B TYR 4.3 0.6 + - - -
754B ILE* 1.3 68.4 - - - +
756B GLN* 1.3 59.3 + - - +
757B GLY 3.5 22.4 - - - +
758B VAL* 5.0 1.8 - - + -
777B VAL* 3.5 12.8 - - + +
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Residues in contact with GLN 756 (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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668B PRO* 3.6 16.3 - - - +
672B TYR* 3.7 27.5 - - - +
674B VAL* 4.0 27.4 - - + +
725B LEU* 3.9 10.4 - - + +
745B LEU* 3.0 5.7 + - + +
747B CYS* 3.6 31.2 + - + +
749B GLU* 4.4 6.7 + - - -
754B ILE* 3.1 37.6 + - - +
755B LEU* 1.3 74.1 - - - +
757B GLY* 1.3 57.6 + - - +
775B VAL 3.7 1.0 - - - +
776B ARG* 3.7 8.0 - - - +
777B VAL* 2.9 25.5 + - - -
778B SER* 4.6 4.5 + - - -
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Residues in contact with GLY 757 (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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725B LEU* 4.3 2.5 - - - -
744B PRO 3.6 0.3 - - - -
745B LEU* 2.8 47.4 + - - +
755B LEU* 3.5 10.3 - - - +
756B GLN* 1.3 81.0 - - - +
758B VAL* 1.3 63.3 + - - -
774B TYR* 4.3 7.4 - - - -
775B VAL 3.2 10.1 - - - -
777B VAL* 3.8 2.2 - - - -
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Residues in contact with VAL 758 (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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591B THR* 5.8 1.8 - - - +
599B LEU* 3.9 23.1 - - + +
600B THR 3.9 16.8 - - - +
601B ALA* 4.2 5.2 - - + +
646B ASP 4.2 6.7 - - - +
647B ILE* 4.2 9.2 - - + -
742B GLY* 3.8 22.0 - - - +
743B GLY 3.5 3.4 - - - +
755B LEU* 5.0 2.9 - - + -
757B GLY* 1.3 73.2 - - - +
759B THR* 1.3 73.6 + - - +
760B SER 3.3 1.7 + - - -
774B TYR* 3.9 2.9 - - - +
775B VAL* 3.2 37.2 + - + +
777B VAL* 3.6 22.7 - - + -
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Residues in contact with THR 759 (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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601B ALA* 4.0 2.9 - - - +
682B ILE* 3.0 29.3 - - + +
738B GLN 3.6 8.1 - - - +
740B ASP 3.4 24.6 + - - +
741B ALA* 3.9 1.5 - - - -
742B GLY* 3.0 24.6 + - - -
743B GLY* 2.9 19.3 + - - -
744B PRO 4.3 0.7 + - - -
757B GLY 4.1 0.2 - - - -
758B VAL* 1.3 73.1 - - - +
760B SER* 1.3 61.4 + - - +
761B TRP* 3.4 32.5 - - + +
774B TYR* 3.1 17.5 - - + -
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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