Contacts of the helix formed by residues 76 - 92 (chain 4) in PDB entry 5LN3
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 SER 76 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414 LYS* 4.2 5.1 + - - +
744 GLU 3.9 1.0 + - - -
754 LEU* 1.4 76.4 - - - +
774 PRO* 1.4 65.8 - - - +
784 THR* 4.1 21.1 - - - -
794 ALA* 3.1 24.6 + - - +
804 ALA* 3.1 10.3 + - - +
1084 ASP* 4.5 1.3 - - - -
1114 GLU* 3.5 20.2 + - - -
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Residues in contact with PRO 77 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414 LYS* 3.8 17.5 - - + -
424 ILE* 4.0 27.2 - - + +
754 LEU 3.8 5.8 - - - +
764 SER* 1.4 77.7 - - - +
784 THR* 1.3 65.5 + - - +
804 ALA* 3.3 11.3 + - + +
814 ALA* 3.1 21.1 + - - +
1044 LEU* 5.1 0.5 - - - +
1064 GLY* 4.2 12.8 - - - -
1074 TYR 3.5 28.5 - - - +
1084 ASP* 3.7 20.2 - - - +
1114 GLU* 5.7 0.2 - - - +
1144 ALA* 5.8 2.7 - - + -
1164 TYR* 4.8 8.7 - - + -
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Residues in contact with THR 78 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764 SER* 4.1 14.6 - - - -
774 PRO* 1.3 78.1 - - - +
794 ALA* 1.3 63.4 + - + +
814 ALA* 3.0 19.1 + - - +
824 ASN* 3.3 22.5 + - - +
1084 ASP* 4.7 7.2 + - - +
1144 ALA* 6.0 2.6 - - - +
1164 TYR* 3.1 34.0 + - - -
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Residues in contact with ALA 79 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754 LEU* 4.4 17.5 - - + -
764 SER* 3.1 24.4 + - - +
784 THR* 1.3 83.6 - - + +
804 ALA* 1.3 61.7 + - - +
824 ASN* 3.5 7.7 + - - +
834 PHE* 3.4 19.6 + - - +
100C GLN 4.8 0.2 - - - +
101C TYR* 4.0 26.2 - - + +
103C GLU* 5.2 8.5 - - + +
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Residues in contact with ALA 80 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384 MET* 4.7 10.5 - - + -
424 ILE* 4.0 16.6 - - + -
644 VAL* 5.5 7.6 - - + -
754 LEU* 5.0 9.4 - - + +
764 SER 3.1 11.1 + - - +
774 PRO* 3.4 15.0 - - + +
794 ALA* 1.3 77.8 - - - +
814 ALA* 1.4 61.2 + - - +
834 PHE* 3.2 9.8 + - - +
844 THR* 3.0 27.9 + - + +
1044 LEU* 4.9 1.6 - - + -
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Residues in contact with ALA 81 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774 PRO 3.1 11.2 + - - +
784 THR* 3.0 11.9 + - - +
804 ALA* 1.4 77.2 - - - +
824 ASN* 1.4 56.8 + - - +
844 THR* 2.8 22.7 + - - -
854 ARG* 3.0 17.3 + - - +
1044 LEU* 4.0 12.1 - - + -
1164 TYR* 4.2 16.4 - - + -
1244 LEU* 3.7 31.6 - - + +
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Residues in contact with ASN 82 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784 THR* 3.3 19.9 + - - +
794 ALA* 3.5 5.4 + - - +
804 ALA 3.3 0.4 - - - -
814 ALA* 1.4 72.0 - - - +
834 PHE* 1.4 59.1 - - - +
854 ARG* 3.3 21.1 + - - +
864 ARG* 2.9 25.6 + - - +
1244 LEU* 3.4 20.1 - - - +
100C GLN 4.0 7.2 - - - +
101C TYR 4.1 5.5 - - - +
102C GLN* 3.4 50.3 + - - +
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Residues in contact with PHE 83 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594 TYR* 5.3 4.0 - - - -
604 ILE* 5.5 2.0 - - + -
634 ASN* 3.5 30.3 - - - -
644 VAL* 5.5 4.5 - - + -
674 TYR* 3.2 22.9 - + - -
754 LEU* 6.5 0.2 - - + -
794 ALA 3.4 11.1 + - - +
804 ALA* 3.2 13.2 + - - +
824 ASN* 1.4 78.3 - - - +
844 THR* 1.3 66.8 + - + +
864 ARG* 3.1 14.5 + - - +
874 ASN* 3.0 40.3 + - - +
100C GLN* 3.8 39.8 + - + +
101C TYR* 3.6 32.5 - + + -
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Residues in contact with THR 84 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384 MET* 4.7 5.2 - - + -
444 LEU* 6.4 0.7 - - + -
564 PHE* 4.4 6.8 - - - -
604 ILE* 3.6 38.6 - - + -
644 VAL* 6.1 0.4 - - + -
804 ALA* 3.0 15.3 + - + +
814 ALA* 2.8 25.5 + - - -
834 PHE* 1.3 74.2 - - + +
854 ARG* 1.4 63.2 + - - +
874 ASN* 3.3 11.8 + - - +
884 LEU* 3.2 23.7 + - - +
1024 LEU* 6.0 2.2 - - + -
1044 LEU* 3.7 14.9 - - + +
1184 MET* 3.6 20.3 - - - +
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Residues in contact with ARG 85 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583 THR 5.0 0.6 + - - -
613 GLN* 3.4 51.5 + - - +
623 THR* 4.4 13.3 + - - +
653 GLN* 5.7 3.8 - - - +
814 ALA 3.0 13.6 + - - +
824 ASN* 3.3 28.6 + - - +
844 THR* 1.4 79.0 + - - +
864 ARG* 1.4 81.2 + - - +
884 LEU* 3.6 2.1 + - - +
894 ALA* 3.0 31.8 + - + +
1184 MET* 3.7 19.3 - - + -
1224 ALA* 4.6 13.3 - - + +
1244 LEU* 4.0 25.2 - - + +
99C LEU 5.1 1.2 + - - -
100C GLN 5.3 0.2 + - - -
102C GLN* 3.2 24.0 + - - -
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Residues in contact with ARG 86 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623 THR* 4.1 27.3 + - - +
663 ARG* 5.5 7.3 - - - +
1033 TYR* 5.6 0.8 + - - -
824 ASN 2.9 17.1 + - - +
834 PHE* 3.1 10.0 + - + +
854 ARG* 1.4 93.7 - - - +
874 ASN* 1.4 64.7 + - - +
894 ALA* 3.4 26.9 + - - +
904 ASP* 3.1 45.4 + - - +
99C LEU* 3.7 27.1 - - - +
100C GLN* 3.7 35.4 + - - +
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Residues in contact with ASN 87 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564 PHE* 4.4 12.6 - - + -
594 TYR* 4.3 20.1 + - + -
604 ILE* 3.8 15.6 - - + +
834 PHE* 3.0 45.6 + - - +
844 THR* 3.3 11.8 + - - +
864 ARG* 1.4 77.0 - - - +
884 LEU* 1.3 60.7 + - - +
904 ASP* 3.2 22.9 + - - +
914 CYS* 3.1 18.6 - - - -
100C GLN* 5.6 4.2 - - - +
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Residues in contact with LEU 88 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564 PHE* 3.4 29.1 - - + -
844 THR 3.2 13.6 + - - +
854 ARG 3.8 4.9 - - - +
874 ASN* 1.3 76.8 - - - +
894 ALA* 1.4 61.0 + - - +
914 CYS* 3.1 20.3 + - - +
924 LEU* 3.3 8.8 + - - +
984 TYR* 3.8 35.4 - - + +
994 HIS* 4.5 2.5 - - - +
1004 VAL* 4.0 10.3 - - + +
1024 LEU* 4.0 10.8 - - + -
1184 MET* 3.6 23.8 - - + -
1194 ASP 4.0 18.6 - - - +
1204 TYR* 5.4 2.0 - - - -
1224 ALA* 4.3 13.0 - - + +
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Residues in contact with ALA 89 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583 THR* 5.2 5.4 - - + -
623 THR* 4.7 6.7 - - - +
1033 TYR* 4.0 13.8 + - - +
854 ARG* 3.0 25.7 + - + +
864 ARG* 3.4 25.1 - - - +
874 ASN 3.3 0.2 - - - -
884 LEU* 1.4 73.1 - - - +
904 ASP* 1.4 60.7 + - - +
924 LEU* 4.0 7.7 - - - +
934 ARG* 3.4 22.5 - - - +
1224 ALA* 4.4 13.8 - - + +
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Residues in contact with ASP 90 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864 ARG* 3.1 37.1 + - - +
874 ASN* 3.2 21.3 + - - +
894 ALA* 1.4 74.4 - - - +
914 CYS* 1.3 68.7 + - - +
924 LEU 3.2 1.2 + - - -
934 ARG* 3.2 20.5 + - - +
944 SER* 3.3 14.8 + - - +
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Residues in contact with CYS 91 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564 PHE* 4.2 7.2 - - - -
874 ASN* 3.1 22.7 - - - -
884 LEU* 3.3 11.7 - - - +
904 ASP* 1.3 84.9 - - - +
924 LEU* 1.4 58.6 - - - +
944 SER* 3.1 21.6 + - - +
964 THR* 3.2 25.8 - - + +
984 TYR* 3.8 44.0 - - + +
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Residues in contact with LEU 92 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563 LEU* 6.3 2.0 - - + -
583 THR* 5.2 5.8 - - + -
1033 TYR* 6.0 5.2 - - + -
884 LEU 3.3 7.5 + - - +
894 ALA* 4.0 12.1 - - - +
914 CYS* 1.4 81.9 - - - +
934 ARG* 1.3 61.8 + - + +
944 SER 3.4 6.8 - - - +
964 THR 5.2 0.6 - - - +
984 TYR 4.5 7.4 - - - +
994 HIS* 4.7 13.9 - - + -
1204 TYR 4.2 13.9 - - - +
1214 LEU* 3.7 36.1 - - + +
1224 ALA* 5.2 3.6 - - + -
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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
------------------------------------------------------------
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