Contacts of the helix formed by residues 245 - 257 (chain 6) 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 245 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1966 GLY 3.9 14.9 + - - +
1976 LYS* 3.4 14.3 + - - +
1986 ALA* 3.1 37.0 + - + +
2386 MET* 5.5 3.0 + - - +
2406 THR* 4.6 2.2 + - - -
2446 MET* 1.3 71.9 - - - +
2466 MET* 1.3 62.6 + - - +
2476 GLU* 3.4 12.0 + - - +
2486 THR* 2.7 36.5 + - - -
2496 ILE* 3.6 23.3 + - - +
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Residues in contact with MET 246 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2446 MET* 3.1 22.6 + - + +
2456 ASP* 1.3 72.0 + - - +
2476 GLU* 1.3 66.7 + - - +
2496 ILE* 3.1 31.7 + - + +
2506 GLU* 2.8 45.0 + - + +
2756 ILE* 3.7 25.8 - - + +
2786 ARG* 3.7 48.2 - - + +
2796 ILE* 3.7 27.8 - - + +
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Residues in contact with GLU 247 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2456 ASP* 3.4 8.9 + - - +
2466 MET* 1.3 77.9 - - - +
2486 THR* 1.3 57.6 + - - +
2506 GLU* 3.2 10.5 + - - +
2516 ALA* 3.0 31.2 + - - +
2546 MET* 5.3 0.7 - - - +
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Residues in contact with THR 248 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1976 LYS* 4.2 15.6 + - - +
1986 ALA* 4.4 19.1 - - + +
2006 ILE* 4.4 29.1 - - + +
2366 ILE* 4.1 6.8 - - + +
2456 ASP* 2.7 34.2 + - - -
2476 GLU* 1.3 77.7 - - - +
2496 ILE* 1.3 62.6 + - - +
2516 ALA* 3.7 6.0 + - - +
2526 SER* 3.3 20.6 + - - -
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Residues in contact with ILE 249 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1986 ALA* 5.6 1.3 - - + -
2086 THR* 4.7 1.0 - - + +
2106 VAL* 3.9 43.5 - - + -
2366 ILE* 4.1 15.7 - - + -
2386 MET* 5.0 6.1 - - + -
2446 MET* 5.2 3.8 - - - -
2456 ASP 3.6 16.1 + - - +
2466 MET* 3.1 37.3 + - + +
2486 THR* 1.3 75.4 - - - +
2506 GLU* 1.3 67.7 + - - +
2526 SER* 3.3 4.5 + - - -
2536 VAL* 2.9 23.1 + - + +
2596 LEU* 4.5 14.8 - - + -
2756 ILE* 4.4 12.3 - - + -
2796 ILE* 4.5 2.5 - - + -
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Residues in contact with GLU 250 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2466 MET* 2.8 53.7 + - + +
2476 GLU* 3.8 8.3 + - - +
2496 ILE* 1.3 73.1 - - - +
2516 ALA* 1.3 53.7 + - - +
2536 VAL* 2.9 7.0 + - - +
2546 MET* 2.8 46.0 + - + +
2786 ARG* 3.9 7.8 + - - +
2796 ILE* 4.3 1.5 - - + +
2826 GLY* 3.8 10.6 - - - -
2836 PRO* 3.4 33.4 - - - +
2846 ALA* 3.8 22.3 - - + +
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Residues in contact with ALA 251 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2476 GLU 3.0 18.1 + - - +
2486 THR* 3.8 7.4 - - - +
2506 GLU* 1.3 76.5 - - - +
2526 SER* 1.3 61.7 + - - +
2546 MET* 3.3 31.4 + - + +
2556 LYS* 3.4 9.5 + - - +
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Residues in contact with SER 252 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2006 ILE* 5.9 1.3 - - - -
2086 THR* 2.4 29.5 + - - +
2346 GLU* 2.9 38.5 + - - +
2366 ILE* 3.9 13.0 - - - -
2486 THR 3.3 10.2 + - - -
2496 ILE 3.3 8.5 + - - -
2516 ALA* 1.3 72.7 - - - +
2536 VAL* 1.3 65.2 + - - +
2556 LYS* 2.9 16.1 + - - +
2566 THR* 2.7 17.7 + - - +
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Residues in contact with VAL 253 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2086 THR* 4.1 11.9 - - + +
2496 ILE* 2.9 13.9 + - + +
2506 GLU* 2.9 13.4 + - - +
2526 SER* 1.3 71.0 - - - +
2546 MET* 1.3 58.0 + - - +
2556 LYS 2.9 2.8 + - - -
2566 THR* 3.1 5.2 - - - -
2576 ASN* 2.7 32.2 + - - +
2586 HIS 4.1 6.1 - - - +
2596 LEU* 3.9 33.9 - - + -
2796 ILE* 4.4 7.2 - - + -
2846 ALA* 4.3 18.2 - - + +
2876 PHE* 4.4 2.5 - - + +
2886 LEU* 3.7 27.1 - - + -
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Residues in contact with MET 254 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2476 GLU 5.3 0.2 - - - +
2506 GLU* 2.8 25.2 + - + +
2516 ALA* 3.3 39.9 - - + +
2526 SER 3.3 0.2 - - - -
2536 VAL* 1.3 70.8 - - - +
2556 LYS* 1.3 56.7 + - - +
2576 ASN* 4.8 4.4 + - - -
2836 PRO* 5.1 13.9 - - + +
2846 ALA* 4.7 6.5 - - + -
2876 PHE* 3.8 58.1 - - + -
311U VAL* 4.2 15.2 - - - +
315U LYS* 5.9 6.3 - - - -
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Residues in contact with LYS 255 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2036 GLN* 3.9 11.3 + - - +
2046 GLY 3.2 11.1 + - - +
2056 THR* 3.7 27.1 - - + +
2346 GLU* 2.6 37.7 + - - -
2516 ALA 3.4 7.6 + - - +
2526 SER* 2.9 9.7 + - - +
2546 MET* 1.3 78.3 - - - +
2566 THR* 1.3 61.7 + - + +
2576 ASN* 3.8 3.2 - - - +
307U LYS* 3.0 24.3 + - - -
311U VAL* 3.9 27.0 - - + +
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Residues in contact with THR 256 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2046 GLY 4.1 11.7 - - - +
2056 THR 3.2 25.2 - - - +
2066 HIS* 3.4 6.6 - - - +
2076 ILE* 3.4 27.4 - - - +
2086 THR* 2.7 30.0 + - - +
2346 GLU* 4.7 0.4 - - + -
2526 SER* 2.7 16.4 + - - +
2536 VAL* 3.1 5.7 - - - -
2556 LYS* 1.3 81.5 - - + +
2576 ASN* 1.3 63.3 + - - +
2586 HIS* 2.8 31.6 + - - -
307U LYS* 4.6 1.3 + - - +
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Residues in contact with ASN 257 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2536 VAL* 2.7 21.3 + - - -
2546 MET 4.8 6.1 + - - -
2556 LYS 4.3 1.6 - - - +
2566 THR* 1.3 76.2 - - - +
2586 HIS* 1.3 70.7 + - + +
2876 PHE* 3.0 29.1 + - - +
2886 LEU* 3.7 6.4 - - - -
2896 ASP* 2.8 47.7 + - - +
2906 ALA 4.1 1.6 + - - -
307U LYS* 3.9 21.0 + - - -
314U ARG* 3.8 17.1 + - - +
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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