Contacts of the helix formed by residues 123 - 136 (chain 0) in PDB entry 5IY8
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 ASN 123 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210 SER* 3.6 1.9 - - - -
1220 GLY* 1.3 75.6 - - - +
1240 PRO* 1.4 66.1 - - - +
1250 ARG* 3.0 36.5 + - - +
1260 LYS* 3.5 25.6 + - + +
1270 HIS* 2.9 21.9 + - - -
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Residues in contact with PRO 124 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920 VAL* 3.7 11.1 - - + +
930 GLU* 5.2 9.9 - - + +
960 PHE* 3.6 36.1 - - + -
1220 GLY 4.0 7.3 - - - +
1230 ASN* 1.4 89.0 - - - +
1250 ARG* 1.3 65.8 + - + +
1260 LYS 3.3 0.2 - - - -
1270 HIS* 3.1 14.2 + - - +
1280 ILE* 3.1 23.7 + - + +
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Residues in contact with ARG 125 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230 ASN* 3.0 21.6 + - - +
1240 PRO* 1.3 81.8 - - + +
1260 LYS* 1.3 55.3 + - + +
1280 ILE* 3.2 23.1 - - + +
1290 THR* 2.9 41.3 + - - +
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Residues in contact with LYS 126 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180 THR* 3.7 16.4 - - + -
1190 GLU* 3.8 26.9 + - - +
1210 SER* 3.7 27.1 - - - +
1230 ASN* 3.8 25.8 - - + +
1250 ARG* 1.3 75.0 - - + +
1270 HIS* 1.3 55.0 + - - +
1290 THR* 3.5 7.1 + - - +
1300 SER* 2.8 38.5 + - - -
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Residues in contact with HIS 127 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920 VAL* 3.9 16.8 - - + -
960 PHE* 3.8 8.8 - + - -
1040 ILE* 2.8 43.3 + - + -
1060 ILE* 3.6 20.5 - - + +
1180 THR* 3.6 18.7 - - + +
1210 SER* 3.2 34.2 + - - -
1230 ASN 2.9 29.2 + - - -
1240 PRO* 3.1 12.4 + - - +
1260 LYS* 1.3 75.4 - - + +
1280 ILE* 1.4 64.1 + - - +
1300 SER* 3.4 1.6 + - - -
1310 LEU* 3.0 31.1 + - - +
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Residues in contact with ILE 128 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890 GLU* 3.8 35.5 - - + +
920 VAL* 4.3 6.3 - - + -
930 GLU* 3.7 44.4 - - + +
1240 PRO* 3.1 18.0 + - + +
1250 ARG* 3.2 39.0 - - + +
1270 HIS* 1.4 74.1 - - - +
1290 THR* 1.3 58.0 + - - +
1310 LEU* 3.3 4.7 + - - +
1320 LYS* 3.0 34.0 + - + +
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Residues in contact with THR 129 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250 ARG* 2.9 29.2 + - - +
1260 LYS* 3.6 7.4 - - - +
1280 ILE* 1.3 77.2 - - - +
1300 SER* 1.4 56.3 + - - +
1320 LYS* 3.3 9.9 + - + +
1330 LYS* 3.0 35.1 + - + +
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Residues in contact with SER 130 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060 ILE* 4.6 3.1 - - - -
1170 LEU* 3.4 23.8 + - - +
1180 THR* 2.8 30.4 + - - +
1260 LYS 2.8 22.7 + - - -
1270 HIS* 3.6 3.8 - - - -
1290 THR* 1.4 73.5 - - - +
1310 LEU* 1.3 56.4 + - - +
1330 LYS* 3.3 5.7 + - - +
1340 ALA* 3.0 31.1 + - - +
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Residues in contact with LEU 131 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630 VAL* 5.9 3.4 - - + -
650 VAL* 5.7 1.6 - - + -
850 LEU* 3.7 39.5 - - + +
880 LEU* 3.7 22.2 - - + +
890 GLU* 3.5 48.6 - - + +
920 VAL* 3.8 18.2 - - + -
1060 ILE* 4.4 24.0 - - + -
1170 LEU* 5.6 4.0 - - + -
1270 HIS 3.0 21.8 + - - +
1280 ILE 3.3 1.1 + - - +
1300 SER* 1.3 74.0 - - - +
1320 LYS* 1.3 61.3 + - - +
1340 ALA* 3.6 3.5 + - - -
1350 VAL* 3.5 16.5 + - - +
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Residues in contact with LYS 132 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890 GLU* 2.7 41.9 + - - +
1280 ILE* 3.0 16.4 + - + +
1290 THR* 3.3 12.5 + - - +
1310 LEU* 1.3 74.2 - - - +
1330 LYS* 1.3 61.0 + - - +
1350 VAL* 3.3 25.4 - - + +
1360 ASP* 4.4 1.9 + - - +
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Residues in contact with LYS 133 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290 THR* 3.0 23.8 + - + +
1300 SER* 3.9 5.6 - - - +
1320 LYS* 1.3 74.8 - - - +
1340 ALA* 1.3 60.4 + - - +
1350 VAL 3.5 0.3 + - - -
1360 ASP* 3.8 15.6 + - - +
1370 MET* 4.2 6.8 - - - +
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Residues in contact with ALA 134 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810 LEU* 4.7 0.7 - - - +
850 LEU* 3.9 19.5 - - + +
1170 LEU* 4.1 17.9 - - + -
1300 SER 3.0 18.2 + - - +
1310 LEU* 3.9 3.1 - - - +
1330 LYS* 1.3 75.2 - - - +
1350 VAL* 1.4 67.1 + - - +
1360 ASP 3.1 1.0 + - - -
1370 MET* 3.1 42.5 + - + +
1380 THR* 3.3 7.6 + - - -
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Residues in contact with VAL 135 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810 LEU* 3.9 19.6 - - + +
820 THR* 4.2 27.6 - - + +
850 LEU* 3.6 17.0 - - + +
1310 LEU 3.5 6.7 + - - +
1320 LYS* 3.3 19.3 - - + +
1330 LYS 3.4 0.4 - - - -
1340 ALA* 1.4 79.6 - - - +
1360 ASP* 1.3 68.7 + - + +
1380 THR* 3.3 18.5 + - - +
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Residues in contact with ASP 136 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320 LYS 5.1 1.3 - - - +
1330 LYS* 3.8 12.1 + - - +
1350 VAL* 1.3 85.6 - - + +
1370 MET* 1.4 58.3 + - + +
1380 THR* 3.4 10.7 - - - +
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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