Contacts of the strand formed by residues 917 - 922 (chain B) in PDB entry 1ED8
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 LEU 917 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 5.6 0.2 - - - -
553B MET 4.8 1.6 - - - +
554B GLY* 4.1 13.9 - - - -
555B ASP* 3.4 11.9 - - - +
583B GLN* 3.3 7.8 - - - -
584B TYR* 3.1 37.7 + - + -
586B HIS* 3.8 11.4 - - + +
867B THR* 3.7 12.3 - - - +
868B ALA* 4.0 15.5 - - + +
870B HIS* 3.2 45.3 - - - +
871B ALA* 3.4 10.5 - - + +
915B SER 4.2 0.4 - - - +
916B GLN* 1.3 78.4 - - - +
918B ARG* 1.3 80.6 + - - +
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Residues in contact with ARG 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 3.4 31.6 + - - +
416A GLN* 4.3 7.5 - - - +
432A LEU* 5.8 4.6 - - - +
553B MET* 5.4 2.2 + - - +
555B ASP* 3.0 24.1 + - - +
558B ILE* 4.1 21.6 - - + +
575B ILE* 2.7 45.6 + - - +
576B ASP* 3.7 20.4 + - - +
578B LEU* 4.4 4.2 + - - +
581B THR* 4.0 8.3 - - - +
582B GLY 3.4 6.5 - - - -
583B GLN* 5.1 0.2 - - - +
866B VAL* 4.7 11.4 + - - +
867B THR* 3.0 22.4 + - - -
917B LEU* 1.3 82.9 - - - +
919B ILE* 1.3 68.6 + - - +
920B ALA* 3.6 24.7 - - - +
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Residues in contact with ILE 919 (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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581B THR* 3.4 2.4 - - - -
582B GLY 2.8 42.4 + - - +
583B GLN 4.1 0.7 - - - +
584B TYR* 3.9 44.6 - - + +
865B ILE* 4.0 17.9 - - + -
866B VAL 3.8 2.9 - - - -
867B THR* 3.7 18.6 - - + +
918B ARG* 1.3 74.7 - - - +
920B ALA* 1.3 65.0 + - - +
929B VAL* 3.8 45.7 - - + +
933B THR* 4.6 4.5 - - - +
938B LEU* 4.4 11.7 - - + -
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Residues in contact with ALA 920 (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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578B LEU* 3.8 16.3 - - + +
580B LEU 3.3 9.9 - - - +
581B THR* 3.9 4.0 - - + -
865B ILE* 3.4 2.8 - - - +
866B VAL 2.7 38.6 + - - +
918B ARG* 3.6 38.8 - - - +
919B ILE* 1.3 78.6 - - - +
921B ALA* 1.3 64.3 + - - +
929B VAL* 4.4 1.6 - - - -
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Residues in contact with ALA 921 (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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578B LEU* 3.8 5.8 - - - +
579B PRO* 3.5 5.2 - - - +
580B LEU* 2.8 38.1 + - - +
863B LEU* 4.2 1.3 - - + -
864B VAL 3.1 13.2 - - - +
865B ILE* 3.8 15.5 - - + -
920B ALA* 1.3 77.5 - - - +
922B TYR* 1.3 61.7 + - - +
926B ALA* 3.6 21.8 - - + -
929B VAL* 3.9 17.2 - - + +
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Residues in contact with TYR 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B MET* 2.2 47.9 + - + +
505B PRO 3.2 30.5 - - - -
506B VAL* 3.7 13.2 - - + -
536B SER* 6.4 0.4 - - - -
578B LEU* 4.1 4.7 - - + -
579B PRO* 3.9 19.1 - - + -
580B LEU* 5.3 0.4 - - - -
853B LEU* 4.0 26.2 - - + -
856B ALA* 4.0 33.2 + - + -
857B LYS* 3.8 16.3 + - + +
862B THR 3.4 2.1 - - - +
863B LEU* 3.5 1.2 - - - +
864B VAL* 2.8 36.3 + - + +
921B ALA* 1.3 76.3 - - - +
923B GLY* 1.3 68.4 + - - +
926B ALA* 4.1 4.3 - - - -
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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
------------------------------------------------------------
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