Contacts of the helix formed by residues 286 - 298 (chain 1) in PDB entry 3EXG
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 286 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431 ARG* 3.2 23.4 + - - -
2601 TYR* 3.1 22.7 + - - +
2821 ARG* 3.4 28.4 + - + +
2831 SER 4.0 1.0 + - - -
2851 SER* 1.3 79.2 + - - +
2871 PRO* 1.3 70.5 - - - +
2881 ILE* 2.6 33.8 + - - +
2891 MET* 3.1 23.5 + - + +
2901 LEU* 3.2 19.9 + - - +
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Residues in contact with PRO 287 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 MET* 3.6 13.0 - - - +
431 ARG* 3.6 4.7 - - - +
671 GLY 3.7 16.8 - - - +
691 GLU* 3.5 28.0 - - + +
701 ALA* 4.0 18.6 - - + +
2281 MET* 3.7 29.1 - - + +
2301 ILE* 5.2 2.3 - - - +
2601 TYR* 3.7 9.0 - - - +
2851 SER 2.9 5.1 - - - +
2861 ASP* 1.3 94.5 - - - +
2881 ILE* 1.3 62.6 + - + +
2901 LEU* 3.7 3.8 - - + +
2911 LEU* 3.4 15.2 + - - +
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Residues in contact with ILE 288 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 TYR* 3.5 31.1 - - + +
391 MET* 3.4 52.9 - - + +
401 GLN* 3.5 29.2 - - + +
431 ARG* 3.8 24.7 - - + +
691 GLU* 5.1 1.1 - - + -
2861 ASP* 2.6 16.9 + - - +
2871 PRO* 1.3 72.9 - - + +
2891 MET* 1.3 66.8 + - - +
2911 LEU* 3.1 4.0 + - - +
2921 LYS* 2.9 24.5 + - + +
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Residues in contact with MET 289 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2821 ARG 4.8 0.2 - - - +
2831 SER 3.2 27.6 - - - +
2841 LYS* 4.4 11.0 - - - +
2851 SER 4.5 1.6 - - - -
2861 ASP* 3.1 19.8 + - + +
2881 ILE* 1.3 81.0 - - - +
2901 LEU* 1.3 94.3 - - + +
2921 LYS* 3.1 12.9 + - + +
2931 ASP* 2.9 55.3 + - - +
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Residues in contact with LEU 290 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2281 MET* 4.4 23.1 - - + +
2291 ASP* 5.1 5.8 - - + +
2301 ILE* 6.5 0.4 - - + -
2841 LYS 4.7 5.6 - - - +
2851 SER* 4.1 17.7 - - - +
2861 ASP 3.2 18.8 + - - +
2871 PRO 3.7 5.4 - - - +
2881 ILE 3.2 0.8 - - - -
2891 MET* 1.3 102.6 - - + +
2911 LEU* 1.3 61.7 + - - +
2931 ASP* 3.5 6.6 + - + +
2941 ARG* 3.3 27.5 + - - +
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Residues in contact with LEU 291 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 LEU* 4.6 18.8 - - + -
321 GLY* 4.2 5.8 - - - +
351 TYR* 3.9 16.4 - - + -
361 TYR* 3.9 26.0 - - + +
391 MET* 3.8 31.6 - - + -
2301 ILE* 3.9 26.2 - - + +
2311 LEU* 5.0 4.5 - - + -
2871 PRO 3.4 4.3 + - - +
2881 ILE 3.1 3.9 + - - +
2901 LEU* 1.3 74.8 - - - +
2921 LYS* 1.3 57.7 + - - +
2941 ARG* 3.5 16.8 + - + +
2951 MET* 2.8 47.5 + - + +
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Residues in contact with LYS 292 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 TYR* 4.3 21.7 - - + +
2881 ILE* 2.9 14.4 + - + +
2891 MET* 3.1 18.4 - - + +
2911 LEU* 1.3 74.4 - - - +
2931 ASP* 1.3 67.9 + - - +
2941 ARG 3.0 0.7 + - - -
2951 MET* 3.0 9.0 + - - +
2961 VAL* 2.8 34.7 + - + +
3031 VAL* 3.4 31.0 - - - +
3061 LEU* 3.5 26.5 - - + -
3071 LYS* 5.8 5.4 - - - +
3101 ASP* 5.4 4.3 - - - -
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Residues in contact with ASP 293 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2891 MET* 2.9 52.4 + - - +
2901 LEU* 3.9 7.4 - - + +
2921 LYS* 1.3 80.1 + - - +
2941 ARG* 1.3 58.1 + - + +
2961 VAL* 4.4 3.2 - - - +
2971 ASN* 3.0 47.2 + - - +
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Residues in contact with ARG 294 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 PHE* 3.6 44.8 - - + +
81 GLU 3.4 20.0 + - - -
91 ILE* 4.6 0.2 - - - +
271 LEU* 5.9 1.1 - - + -
2291 ASP* 2.7 37.5 + - - -
2301 ILE* 5.0 2.8 - - - +
2311 LEU* 2.9 34.4 - - - +
2901 LEU* 3.3 17.1 + - - +
2911 LEU* 3.8 15.9 - - + +
2921 LYS 3.1 1.2 - - - -
2931 ASP* 1.3 74.4 - - + +
2951 MET* 1.3 68.7 + - - +
2971 ASN* 5.2 0.9 - - - -
2981 SER* 3.1 31.5 + - - -
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Residues in contact with MET 295 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271 LEU* 4.4 5.2 - - - -
291 ARG 4.5 3.4 - - - +
321 GLY* 3.0 44.2 - - - +
331 LEU* 3.4 25.8 - - + +
361 TYR* 4.6 2.7 - - + -
2911 LEU* 2.8 29.6 - - + +
2921 LYS* 3.4 7.9 - - - +
2941 ARG* 1.3 77.5 - - - +
2961 VAL* 1.3 59.3 + - - +
2991 ASN 3.7 0.2 + - - -
3001 LEU* 2.8 54.1 + - - +
3011 ALA* 3.0 23.5 - - + +
3061 LEU* 4.5 15.7 - - + -
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Residues in contact with VAL 296 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2921 LYS* 2.8 24.4 + - + +
2931 ASP* 4.4 3.4 - - - +
2941 ARG 3.1 0.4 + - - -
2951 MET* 1.3 68.5 - - - +
2971 ASN* 1.3 71.9 + - - +
2981 SER 2.6 17.1 + - - -
2991 ASN* 2.8 17.2 + - - -
3011 ALA 3.6 7.5 - - - +
3021 SER* 4.6 0.7 - - - +
3031 VAL* 3.7 41.3 - - + +
3061 LEU* 4.3 7.4 - - + -
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Residues in contact with ASN 297 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2931 ASP* 3.0 35.6 + - - +
2941 ARG* 5.2 0.4 - - - -
2961 VAL* 1.3 86.9 - - - +
2981 SER* 1.3 56.7 + - - +
2991 ASN 3.5 0.8 + - - -
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Residues in contact with SER 298 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21 ALA* 4.3 5.5 - - - +
51 ALA* 3.7 15.8 - - - +
71 PHE* 3.7 19.1 - - - -
2941 ARG* 3.1 17.2 + - - -
2961 VAL 2.6 6.9 + - - -
2971 ASN* 1.3 75.4 - - - +
2991 ASN* 1.3 69.9 + - - +
3001 LEU* 3.3 20.0 - - - +
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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