Contacts of the helix formed by residues 871 - 884 (chain D) in PDB entry 3JW0
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 ASP 871 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.4 14.6 - - - +
27A GLY* 3.6 26.2 - - - +
869D LEU 3.5 2.9 + - - -
870D MET* 1.3 76.8 - - - +
872D ALA* 1.3 66.0 + - - +
873D GLU* 3.1 29.6 + - - +
874D LYS* 3.6 26.8 - - - +
875D ARG* 3.2 17.5 + - - +
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Residues in contact with ALA 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.4 13.0 - - + +
27A GLY* 5.2 6.3 - - - -
835D LEU* 4.1 10.3 - - + -
837D ASP* 2.8 42.1 - - - +
838D VAL 6.3 0.2 - - - +
871D ASP* 1.3 77.9 - - - +
873D GLU* 1.3 67.1 + - - +
875D ARG* 2.8 28.2 + - - +
876D ILE* 3.2 9.1 + - - +
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Residues in contact with GLU 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835D LEU* 5.1 6.1 - - + +
871D ASP* 3.1 13.9 + - - +
872D ALA* 1.3 76.6 - - - +
874D LYS* 1.3 76.6 + - - +
876D ILE* 2.9 24.0 + - - +
877D ARG* 3.3 47.0 + - - +
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Residues in contact with LYS 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870D MET* 4.0 25.7 - - + +
871D ASP* 3.6 21.0 + - - +
872D ALA 3.4 0.4 - - - -
873D GLU* 1.3 90.8 - - - +
875D ARG* 1.3 60.4 + - - +
877D ARG* 3.5 12.6 + - + +
878D LEU* 3.3 22.7 + - - +
938D ARG* 6.1 1.0 - - - +
942D LEU* 4.1 21.8 - - + +
945D VAL* 3.8 9.0 - - + +
946D GLU* 3.2 33.7 + - + +
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Residues in contact with ARG 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.8 14.1 - - - +
34A GLN* 3.0 27.0 + - - +
837D ASP* 6.4 1.1 - - - +
838D VAL* 3.9 22.4 + - + +
840D VAL* 3.4 30.5 - - - +
843D TRP* 3.7 26.9 - - + -
867D VAL* 3.3 16.2 + - + +
868D LEU* 2.8 22.1 + - - +
870D MET* 2.6 34.1 + - + +
871D ASP 3.2 11.4 + - - +
872D ALA* 2.8 18.0 + - - +
874D LYS* 1.3 78.3 - - - +
876D ILE* 1.3 58.4 + - - +
878D LEU* 3.9 2.5 - - + +
879D LEU* 3.4 15.4 + - - +
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Residues in contact with ILE 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835D LEU* 4.1 14.8 - - + -
836D GLY* 3.1 35.0 - - - +
837D ASP* 4.1 10.3 - - - +
838D VAL* 4.0 10.8 - - + -
872D ALA 3.6 12.6 - - - +
873D GLU* 2.9 9.5 + - - +
875D ARG* 1.3 77.4 - - - +
877D ARG* 1.3 66.7 + - - +
878D LEU 3.3 0.2 - - - -
879D LEU* 3.2 7.4 + - + +
880D GLN* 3.0 19.6 + - - +
886D SER* 3.3 39.7 - - - +
887D ARG* 5.2 4.7 - - - +
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Residues in contact with ARG 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873D GLU* 3.4 36.4 + - - +
874D LYS* 3.7 8.3 - - + +
875D ARG 3.5 0.2 - - - -
876D ILE* 1.3 77.0 - - + +
878D LEU* 1.3 50.0 + - - +
880D GLN* 2.7 39.2 + - - +
881D PHE* 2.7 21.0 + - - +
886D SER* 6.1 0.2 - - - -
945D VAL* 3.4 33.4 + - + +
946D GLU* 3.8 28.4 + - - +
948D ALA* 3.3 28.8 + - - +
949D GLN 5.6 0.6 - - - -
8Y LEU* 4.3 7.9 - - - +
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Residues in contact with LEU 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843D TRP* 4.1 19.1 - - + -
863D PHE* 4.2 15.3 - - + -
867D VAL* 4.2 23.6 - - + -
870D MET* 4.3 16.4 - - - -
874D LYS 3.3 13.0 + - - +
875D ARG* 3.9 5.4 - - - +
877D ARG* 1.3 80.6 - - - +
879D LEU* 1.3 63.8 + - - +
880D GLN 3.0 1.4 + - - -
881D PHE* 3.2 11.3 + - + +
882D VAL* 3.2 39.0 + - + +
905D PHE* 5.8 0.2 - - + -
926D LEU* 5.1 2.5 - - + -
941D LEU* 4.3 19.3 - - + -
945D VAL* 3.6 26.8 - - + +
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Residues in contact with LEU 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838D VAL* 4.0 15.0 - - + -
843D TRP* 3.8 21.5 - - + +
875D ARG 3.4 12.8 + - - +
876D ILE* 3.2 9.3 + - + +
878D LEU* 1.3 78.7 - - - +
880D GLN* 1.3 52.5 + - - +
882D VAL* 4.0 1.8 - - - +
883D THR* 2.5 54.6 + - + +
885D THR 4.0 6.3 - - - +
886D SER 4.1 16.4 - - - +
887D ARG 4.2 7.6 - - - +
888D VAL* 3.5 29.2 - - + -
893D PHE* 3.7 26.0 - - + -
896D LEU* 5.0 0.4 - - + -
905D PHE* 5.0 0.4 - - + -
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Residues in contact with GLN 880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876D ILE 3.0 10.4 + - - +
877D ARG* 2.7 28.8 + - - +
879D LEU* 1.3 68.1 - - - +
881D PHE* 1.3 55.4 + - - +
882D VAL 2.6 16.0 + - - -
884D GLY* 2.6 37.9 + - - +
885D THR* 3.0 22.3 + - - +
886D SER* 3.8 24.5 + - - +
921D THR* 4.5 0.7 - - - +
948D ALA* 6.0 1.7 - - - +
949D GLN 4.6 18.4 + - - -
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Residues in contact with PHE 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877D ARG 2.7 18.6 + - - +
878D LEU* 3.6 15.9 - - + +
880D GLN* 1.3 73.2 + - - +
882D VAL* 1.3 66.5 + - + +
917D PRO* 3.7 23.6 - - + -
918D ARG 4.2 1.1 - - - -
919D ALA* 3.2 32.3 - - + +
921D THR* 3.8 10.5 - - - +
926D LEU* 4.0 15.9 - - + -
941D LEU* 6.2 0.4 - - + -
944D ALA* 4.4 16.6 - - + +
945D VAL* 5.3 4.7 - - + +
948D ALA* 4.0 29.6 - - + -
73Y LEU* 3.6 33.9 - - + -
74Y ARG* 4.3 14.8 - - + +
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Residues in contact with VAL 882 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878D LEU* 3.2 21.0 + - + +
879D LEU 4.0 1.1 - - - +
880D GLN 2.6 6.0 + - - -
881D PHE* 1.3 83.0 - - + +
883D THR* 1.3 60.2 + - - +
884D GLY 3.4 0.7 - - - -
905D PHE* 3.1 42.2 - - + -
919D ALA* 4.0 4.0 - - + -
920D HIS 4.1 0.3 - - - -
921D THR* 3.3 23.0 + - - -
924D ASN* 3.6 7.4 - - - -
925D ARG 3.7 28.1 + - - +
926D LEU* 3.9 26.7 - - + -
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Residues in contact with THR 883 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D ASP* 5.4 4.3 - - - +
879D LEU* 2.5 41.7 + - + +
882D VAL* 1.3 75.9 - - - +
884D GLY* 1.3 58.1 + - - +
885D THR* 3.0 31.8 + - - +
896D LEU* 3.9 19.7 - - + -
905D PHE* 4.4 9.0 - - + -
921D THR* 3.0 19.0 - - - +
924D ASN* 3.1 33.2 - - + +
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Residues in contact with GLY 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D ASP 5.8 0.2 - - - -
880D GLN* 2.6 33.4 + - - +
882D VAL 3.4 1.0 - - - -
883D THR* 1.3 72.7 - - - +
885D THR* 1.3 58.0 + - - +
921D THR* 4.1 16.4 - - - +
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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
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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