Contacts of the helix formed by residues 783 - 794 (chain J) in PDB entry 4XLN
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 ARG 783 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684I PHE* 3.7 15.3 - - + -
685I GLU* 3.3 34.4 + - - +
874I LEU* 3.5 19.1 - - + -
782J SER* 1.3 85.2 + - - +
784J ASP* 1.3 67.1 + - - +
786J ILE* 3.4 14.3 + - - +
787J LEU* 3.2 19.1 + - - +
1027J GLY 4.4 3.4 + - - -
1028J ALA* 2.6 45.4 + - - +
1029J ARG* 3.0 44.7 - - - +
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Residues in contact with ASP 784 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678I PRO* 3.3 28.1 - - - +
681I GLY* 5.0 2.2 - - - -
683I ASN* 4.2 4.3 - - - +
684I PHE* 3.4 33.0 - - - -
872I ASN* 3.6 6.2 + - - +
874I LEU* 3.3 23.5 - - - +
782J SER 3.1 1.6 + - - -
783J ARG* 1.3 75.5 - - - +
785J ILE* 1.3 63.1 + - - +
787J LEU* 2.9 16.9 + - - +
788J GLY 2.9 1.2 + - - -
939J PHE* 3.4 24.2 - - + -
942J SER* 2.7 25.8 + - - +
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Residues in contact with ILE 785 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684I PHE* 6.0 0.9 - - + -
730J PRO* 5.7 1.6 - - + -
731J LEU* 3.7 30.7 - - + -
781J PRO* 3.7 20.2 - - + -
782J SER* 3.8 15.9 - - - +
783J ARG 3.4 0.4 - - - -
784J ASP* 1.3 74.6 - - - +
786J ILE* 1.3 66.2 + - - +
788J GLY* 3.1 1.0 + - - -
789J LEU* 2.9 34.1 + - + +
934J LEU 3.4 25.6 - - - +
935J LYS* 3.7 23.3 - - + +
938J GLY* 4.3 9.9 - - - -
939J PHE* 3.5 24.6 - - + -
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Residues in contact with ILE 786 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781J PRO* 3.2 35.7 - - + +
782J SER* 3.6 13.5 - - - +
783J ARG 3.6 10.3 - - - +
784J ASP 3.3 0.2 - - - -
785J ILE* 1.3 74.4 - - - +
787J LEU* 1.3 57.2 + - - +
789J LEU* 3.8 0.3 - - - +
790J TYR* 2.9 32.9 + - - +
906J GLN 4.4 0.9 - - - +
907J GLU* 4.0 6.7 - - - -
908J LYS* 3.5 32.5 - - + +
911J LEU* 4.4 9.9 - - + -
1026J SER* 3.2 33.0 - - - +
1027J GLY 4.0 17.5 - - - +
1028J ALA 4.5 2.0 - - - +
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Residues in contact with LEU 787 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678I PRO* 4.3 19.5 - - + -
874I LEU* 4.6 7.2 - - + -
783J ARG 3.2 8.6 + - - +
784J ASP* 2.9 15.9 + - - +
786J ILE* 1.3 79.4 - - - +
788J GLY* 1.3 54.8 + - - +
790J TYR* 3.4 4.8 - - - +
791J TYR* 2.9 28.9 + - - +
942J SER* 5.1 3.4 - - - -
945J SER* 5.7 0.2 - - - +
947J ILE* 3.7 29.6 - - + -
1022J VAL* 3.6 29.4 - - + -
1023J MET* 4.0 41.1 - - + -
1026J SER* 4.4 7.9 - - - +
1028J ALA* 4.3 4.4 - - + +
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Residues in contact with GLY 788 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784J ASP 2.9 10.7 + - - -
785J ILE 3.7 0.4 - - - -
787J LEU* 1.3 72.6 - - - +
789J LEU* 1.3 62.8 + - - +
790J TYR 3.0 4.5 - - - -
791J TYR* 3.0 6.5 + - - +
792J ILE* 3.0 28.2 + - - +
938J GLY 3.8 1.3 - - - -
941J LEU* 4.1 8.5 - - - -
942J SER* 3.0 34.7 + - - -
945J SER* 5.4 0.2 - - - -
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Residues in contact with LEU 789 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781J PRO* 4.8 0.4 - - + -
785J ILE* 2.9 35.9 + - + +
786J ILE 4.2 2.5 - - - +
788J GLY* 1.3 73.5 - - - +
790J TYR* 1.3 51.0 + - - +
792J ILE* 3.5 6.4 - - + +
793J THR* 2.6 36.4 + - - +
882J PHE* 4.3 23.8 - - + -
885J ILE* 5.1 8.1 - - + -
906J GLN* 3.9 5.8 - - + +
911J LEU* 3.7 25.6 - - + -
934J LEU* 4.0 28.7 - - + +
937J TYR* 5.2 0.9 - - + -
938J GLY* 3.7 23.7 + - - +
941J LEU* 3.8 13.7 - - + -
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Residues in contact with TYR 790 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE 2.9 19.8 + - - +
787J LEU* 3.4 3.8 - - - +
789J LEU* 1.3 73.8 - - - +
791J TYR* 1.3 62.2 + - - +
792J ILE 3.1 1.6 - - - -
793J THR* 2.9 4.4 + - - -
794J GLN* 2.8 66.1 + - + +
905J PRO* 4.0 17.4 - - + +
906J GLN 3.3 22.6 + - - +
907J GLU* 4.0 8.7 - - + -
1016J PRO 5.4 0.9 + - - -
1021J TYR* 5.3 5.5 - - - -
1022J VAL* 3.5 40.9 - - + +
1025J GLN* 4.5 13.2 - - + +
1026J SER* 3.6 30.5 - - - -
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Residues in contact with TYR 791 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946I ARG* 3.3 24.6 + - - -
984I GLU* 3.4 29.0 + - - +
787J LEU 2.9 18.1 + - - +
788J GLY* 3.5 4.9 - - - +
790J TYR* 1.3 83.2 - - + +
792J ILE* 1.3 75.4 + - + +
794J GLN* 3.9 8.5 + - - +
860J LEU* 5.3 2.2 - - + -
861J GLN* 3.6 34.4 + - - +
941J LEU 4.4 4.3 - - - -
944J THR* 5.2 0.7 - - - -
945J SER* 3.5 38.4 + - - -
947J ILE* 4.5 18.8 - - + -
1017J PHE* 4.0 21.4 - + - -
1022J VAL* 5.9 0.7 - - + -
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Residues in contact with ILE 792 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788J GLY 3.0 14.4 + - - +
789J LEU* 3.5 15.7 - - + +
791J TYR* 1.3 92.9 - - + +
793J THR* 1.3 72.2 + - + +
794J GLN 3.6 4.0 + - - +
860J LEU* 4.0 21.9 - - + +
861J GLN* 4.4 4.7 - - - +
876J SER* 4.6 0.5 + - - -
878J GLY* 3.4 42.2 - - - +
881J LEU* 4.4 11.7 - - + -
882J PHE* 4.5 13.5 - - + +
885J ILE* 4.9 1.3 - - + -
941J LEU* 3.6 48.5 - - + -
944J THR* 5.8 0.2 - - - +
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Residues in contact with THR 793 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789J LEU 2.6 25.9 + - - +
790J TYR* 3.0 7.4 + - - -
792J ILE* 1.3 80.0 - - + +
794J GLN* 1.3 62.2 + - - +
795J VAL* 4.1 1.6 - - - +
876J SER* 4.3 2.1 + - - -
878J GLY 4.1 7.2 - - - +
879J ARG* 2.9 51.2 + - - +
882J PHE* 3.8 25.1 - - + -
905J PRO* 3.8 1.4 - - - +
906J GLN* 2.9 37.1 + - + -
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Residues in contact with GLN 794 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790J TYR* 2.8 51.2 + - + +
791J TYR* 4.0 9.6 - - - +
792J ILE 3.3 0.8 - - - -
793J THR* 1.3 78.4 + - - +
795J VAL* 1.3 70.0 + - - +
797J LYS* 6.2 0.2 - - - -
861J GLN* 3.2 28.8 - - - +
876J SER* 4.9 0.2 + - - -
905J PRO* 3.4 23.6 - - + +
1016J PRO* 4.7 12.9 - - - +
1017J PHE* 3.5 36.0 - - + -
1022J VAL* 6.2 0.2 - - - -
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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