Contacts of the helix formed by residues 801 - 810 (chain B) in PDB entry 4CEJ
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 CYS 801 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B THR 3.1 8.7 + - - +
798B PHE* 3.2 4.5 + - - -
800B ALA* 1.3 81.4 - - + +
802B PRO* 1.3 72.3 - - - +
803B PHE* 3.6 9.6 - - - -
804B SER* 2.5 43.8 + - - +
805B HIS 3.3 2.4 + - - -
1110B ILE* 4.3 0.4 - - - -
1111B GLU 3.9 23.8 - - - +
1112B PRO* 4.5 1.1 - - + -
2160B SF4 2.3 42.6 - - - -
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Residues in contact with PRO 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798B PHE* 3.4 42.7 - - + +
801B CYS* 1.3 81.8 - - + +
803B PHE* 1.3 57.0 + - - +
805B HIS* 3.1 8.5 + - - +
806B PHE* 2.9 24.8 + - - +
1107B ARG* 4.0 11.8 - - + +
1108B VAL* 3.9 4.4 - - - -
1109B SER* 3.2 40.8 - - - +
1111B GLU* 4.0 22.4 - - + +
1142B ARG* 4.5 4.0 - - - +
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Residues in contact with PHE 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ARG* 3.8 27.6 - - - -
655A GLU* 4.1 10.1 - - + -
658A LEU* 5.6 1.3 - - + -
772B VAL* 4.2 4.0 - - + -
801B CYS* 3.3 7.1 - - - -
802B PRO* 1.3 76.1 - - - +
804B SER* 1.3 61.7 + - - +
806B PHE* 2.9 26.0 + + - +
807B ALA* 2.9 34.2 + - + +
811B LEU* 6.0 0.7 - - + -
1108B VAL 3.3 23.8 + - - +
1109B SER 3.1 5.3 + - - +
1110B ILE* 3.7 23.6 - - + -
1126B PHE* 4.8 1.6 - - + -
1129B VAL* 3.8 25.4 - - + -
1130B CYS* 3.7 33.7 - - + -
2160B SF4 3.9 7.9 - - - -
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Residues in contact with SER 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B THR* 3.4 18.4 + - - +
800B ALA* 5.1 1.4 - - - +
801B CYS* 2.5 34.8 + - - +
803B PHE* 1.3 78.5 - - - +
805B HIS* 1.3 57.2 + - - +
807B ALA 3.4 0.2 + - - -
808B SER* 2.9 30.8 + - - -
1124B CYS* 4.1 10.1 - - - -
1126B PHE* 3.8 12.7 - - - -
2160B SF4 3.9 27.6 - - - -
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Residues in contact with HIS 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B TYR* 4.2 15.4 + + - -
794B ARG* 3.0 60.9 + - + +
797B THR* 3.8 8.1 - - + -
798B PHE* 3.7 37.8 - - + +
802B PRO 3.1 9.2 + - - +
804B SER* 1.3 81.9 + - - +
806B PHE* 1.3 58.8 + - - +
808B SER* 4.2 2.0 - - - -
809B HIS* 2.8 34.3 + + + +
810B GLY 3.5 2.8 + - - -
1103B ILE* 3.5 33.5 - - + +
1107B ARG 5.6 1.4 + - - -
1108B VAL* 6.3 0.2 - - - +
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Residues in contact with PHE 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A GLU* 3.6 37.7 - - + -
658A LEU* 4.6 3.4 - - + -
659A SER* 4.1 1.1 - - - -
775B LEU* 3.9 13.9 - - + -
783B LEU* 3.8 24.2 - - + -
784B TYR* 3.4 21.5 - - - -
802B PRO 2.9 9.7 + - - +
803B PHE* 2.9 30.5 + + - +
805B HIS* 1.3 76.6 + - - +
807B ALA* 1.3 63.3 + - - +
810B GLY* 3.0 7.3 + - - +
811B LEU* 2.9 59.4 + - + +
1108B VAL* 3.6 28.0 - - + -
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Residues in contact with ALA 807 (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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803B PHE* 2.9 24.4 + - + +
806B PHE* 1.3 77.2 - - - +
808B SER* 1.3 65.2 + - - +
811B LEU* 3.7 8.5 + - + -
812B HIS 3.2 5.2 + - - -
813B LEU* 3.2 38.2 + - + +
1126B PHE* 3.6 39.3 - - + -
1129B VAL* 5.2 0.9 - - + -
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Residues in contact with SER 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B THR* 4.8 5.6 - - - +
804B SER 2.9 20.4 + - - -
805B HIS* 3.9 1.3 - - - -
807B ALA* 1.3 82.8 - - - +
809B HIS* 1.3 83.6 + - - +
812B HIS* 3.0 24.9 + - - -
813B LEU 4.9 2.0 - - - +
1126B PHE* 3.9 18.2 - - - -
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Residues in contact with HIS 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LEU 5.3 0.9 - - - +
784B TYR* 4.2 10.5 - - - -
791B SER* 5.1 3.6 - - - -
793B SER* 5.3 0.6 - - - -
794B ARG* 3.6 60.1 + - + +
797B THR* 4.4 9.7 + - + -
805B HIS* 2.8 34.2 + + - +
808B SER* 1.3 94.2 + - - +
810B GLY* 1.3 59.0 + - - +
812B HIS* 3.2 26.6 + - - +
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Residues in contact with GLY 810 (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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662A ARG* 3.9 1.6 - - - +
783B LEU* 3.7 26.8 - - - +
784B TYR* 3.4 24.4 - - - -
805B HIS 3.5 3.2 + - - -
806B PHE 3.0 13.6 + - - -
809B HIS* 1.3 77.7 - - - +
811B LEU* 1.3 59.2 + - - -
812B HIS* 3.1 21.4 + - - -
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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