Contacts of the strand formed by residues 247 - 256 (chain 1) in PDB entry 1W58
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 GLY 247 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1811 LYS* 4.8 10.8 - - - -
1841 THR* 5.0 2.6 - - - +
1851 ASP 3.3 9.4 + - - -
1861 THR* 3.6 0.7 - - - -
1871 LEU* 2.8 32.7 + - - +
2451 ASN* 3.2 5.4 + - - +
2461 GLY* 1.3 76.0 - - - +
2481 LEU* 1.3 57.8 + - - -
3411 GLN* 3.8 17.9 - - - -
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Residues in contact with LEU 248 (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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1771 LEU* 5.7 1.1 - - + -
1811 LYS* 4.7 5.8 - - - +
1871 LEU* 3.3 17.3 - - + +
1891 VAL* 3.0 35.7 - - + -
2461 GLY 3.7 0.2 - - - -
2471 GLY* 1.3 72.1 - - - -
2491 ALA* 1.3 73.9 + - - +
2501 MET* 4.9 3.6 - - + -
3391 GLY 3.3 6.8 + - - -
3401 VAL* 3.1 26.9 + - + +
3411 GLN* 3.2 32.8 + - + +
3441 ILE* 4.1 22.9 - - + -
3461 PHE* 3.6 36.3 - - + -
3511 LEU* 5.1 2.5 - - + -
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Residues in contact with ALA 249 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1861 THR* 4.1 10.8 - - - +
1871 LEU 2.8 15.7 + - - +
1881 VAL* 4.1 11.4 - - + -
1891 VAL* 3.1 27.7 + - - +
2481 LEU* 1.3 75.7 - - - +
2501 MET* 1.3 69.3 + - - +
3361 VAL* 4.0 20.9 - - + -
3371 ILE 3.4 13.2 - - - +
3381 THR* 4.1 9.0 - - + -
3401 VAL* 4.5 0.4 - - - -
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Residues in contact with MET 250 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1891 VAL* 4.2 17.7 - - + +
1911 PRO* 5.3 4.7 - - - -
2481 LEU* 4.9 4.0 - - + -
2491 ALA* 1.3 80.7 - - - +
2511 ILE* 1.3 67.6 + - - +
2741 LEU 4.3 8.7 - - - +
2751 LEU* 4.0 17.5 - - + +
2761 ASP* 3.8 23.6 - - - +
2771 VAL* 3.3 22.4 - - + -
3361 VAL* 3.6 3.2 - - - -
3371 ILE* 3.1 31.1 + - - +
3401 VAL* 4.1 8.5 - - + +
3441 ILE* 3.2 42.4 - - + -
3511 LEU* 5.0 13.5 - - + -
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Residues in contact with ILE 251 (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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1881 VAL* 3.5 27.6 - - + -
1891 VAL 4.8 1.6 + - - +
1901 ILE* 3.3 31.0 - - + -
2141 VAL* 4.9 1.8 - - + -
2181 ALA* 5.0 9.0 - - + -
2501 MET* 1.3 80.3 - - - +
2521 GLY* 1.3 68.3 + - - +
2531 ILE* 4.3 13.7 - - + -
2741 LEU* 3.2 32.4 + - + +
2751 LEU* 3.0 33.3 + - - -
3341 LEU* 4.5 8.3 - - + -
3351 LEU 3.0 13.7 - - - +
3361 VAL* 4.4 11.0 - - + -
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Residues in contact with GLY 252 (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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2511 ILE* 1.3 78.2 - - - +
2531 ILE* 1.3 67.9 + - - +
2691 ALA* 3.5 24.1 - - - +
2721 SER* 3.8 7.9 - - - -
2741 LEU* 4.7 0.4 - - - -
2751 LEU* 4.5 4.0 - - - -
3331 VAL 3.8 1.6 - - - +
3341 LEU* 3.8 0.5 - - - +
3351 LEU* 3.0 33.6 + - - +
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Residues in contact with ILE 253 (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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2141 VAL* 4.6 24.2 - - + +
2171 ASN* 4.3 23.3 - - + -
2181 ALA* 5.1 1.6 - - + +
2511 ILE* 4.3 9.2 - - + +
2521 GLY* 1.3 80.3 - - - +
2541 GLY* 1.3 67.3 + - - +
2551 GLU* 6.0 2.2 - - - +
2681 MET* 3.9 15.3 - - + +
2691 ALA* 3.6 9.1 + - - -
2721 SER* 3.8 13.2 + - - +
2741 LEU* 4.9 8.7 - - + +
3321 ARG* 4.5 18.2 - - + -
3331 VAL 3.5 7.6 - - - +
3341 LEU* 4.2 20.0 - - + -
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Residues in contact with GLY 254 (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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2531 ILE* 1.3 77.1 - - - +
2551 GLU* 1.3 60.0 + - - +
2651 ALA* 3.4 22.0 - - - -
2681 MET* 3.3 17.3 - - - -
2691 ALA* 3.6 3.3 - - - +
3321 ARG* 3.6 2.3 - - - +
3331 VAL 2.7 36.3 + - - +
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Residues in contact with GLU 255 (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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2531 ILE* 6.0 2.4 - - - +
2541 GLY* 1.3 77.0 - - - +
2561 SER* 1.3 60.2 + - - +
2641 GLU* 5.2 0.7 - - - +
2651 ALA* 3.6 9.5 - - - +
2681 MET* 3.3 27.1 - - + +
3271 LEU* 5.5 1.6 - - - +
3301 THR* 3.8 18.2 - - + +
3311 VAL 3.2 15.3 - - - +
3321 ARG* 3.7 32.6 + - + +
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Residues in contact with SER 256 (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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2551 GLU* 1.3 75.0 - - - +
2571 ASP* 1.3 58.3 + - - +
2581 SER* 2.9 26.5 + - - -
2611 ARG* 3.2 39.3 - - - +
2641 GLU* 3.3 22.7 + - - +
2651 ALA* 3.8 1.7 - - - +
3301 THR* 3.0 19.9 - - - +
3311 VAL* 3.2 18.7 + - - +
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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