Contacts of the helix formed by residues 296 - 309 (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 THR 296 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2311 LEU* 4.3 5.8 - - - -
2941 ASP 4.5 4.3 - - - +
2951 LEU* 1.3 80.6 - - - +
2971 LEU* 1.3 62.9 + - - +
2981 GLU* 2.8 32.4 + - + +
2991 GLU* 2.9 49.5 + - + +
3001 ALA* 3.3 9.4 + - - +
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Residues in contact with LEU 297 (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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2311 LEU* 3.4 49.8 - - + +
2321 ILE* 5.0 10.5 - - + -
2961 THR* 1.3 74.4 + - - +
2981 GLU* 1.3 60.5 + - - +
3001 ALA* 3.7 10.2 - - - +
3011 ARG* 3.0 62.3 + - - +
3191 TRP* 5.1 4.4 - - + -
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Residues in contact with GLU 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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2961 THR* 2.8 22.4 - - + +
2971 LEU* 1.3 81.5 - - - +
2991 GLU* 1.3 64.3 + - + +
3011 ARG* 3.4 20.8 + - - +
3021 GLU* 3.1 21.1 + - - +
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Residues in contact with GLU 299 (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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2591 GLU 5.2 2.3 - - - +
2611 ARG* 2.6 55.5 + - - +
2621 ALA* 3.6 19.8 + - + +
2891 VAL* 5.4 1.8 - - + -
2941 ASP 3.8 0.5 - - - +
2951 LEU* 3.7 12.3 - - + +
2961 THR* 2.9 36.3 + - + +
2981 GLU* 1.3 74.7 - - + +
3001 ALA* 1.3 66.0 + - - +
3021 GLU* 3.3 8.4 + - - +
3031 VAL* 3.0 28.3 + - - +
3311 VAL* 4.5 1.7 - - + +
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Residues in contact with ALA 300 (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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2891 VAL* 3.6 31.9 - - + +
2951 LEU* 5.3 0.6 - - + +
2961 THR 3.3 8.5 + - - +
2971 LEU* 3.7 12.1 - - - +
2991 GLU* 1.3 79.5 - - - +
3011 ARG* 1.3 57.1 + - - +
3031 VAL* 3.0 8.6 - - - +
3041 VAL* 2.9 32.8 + - - +
3191 TRP* 3.8 22.0 - - + -
3211 ALA* 4.2 5.8 - - + -
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Residues in contact with ARG 301 (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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2321 ILE* 5.5 3.2 - - - +
2971 LEU* 3.0 53.1 + - - +
2981 GLU* 3.5 19.5 + - - +
2991 GLU 3.2 0.2 - - - -
3001 ALA* 1.3 76.1 - - - +
3021 GLU* 1.3 65.4 + - - +
3041 VAL* 3.3 8.5 + - + +
3051 ALA* 3.0 26.0 + - + +
3191 TRP* 4.1 28.8 - - - -
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Residues in contact with GLU 302 (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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2621 ALA* 3.9 15.3 - - + +
2631 LYS* 2.8 49.7 + - - +
2981 GLU 3.1 12.9 + - - +
2991 GLU* 3.3 11.4 + - - +
3011 ARG* 1.3 75.3 - - - +
3031 VAL* 1.3 59.2 + - - +
3051 ALA* 3.9 4.6 - - - +
3061 THR* 2.6 39.4 + - - +
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Residues in contact with VAL 303 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2621 ALA* 4.0 11.9 - - + -
2661 VAL* 3.1 38.1 - - + +
2871 ILE* 3.9 24.9 - - + -
2891 VAL* 4.5 10.3 - - + -
2991 GLU 3.0 18.5 + - - +
3001 ALA* 3.0 11.2 - - - +
3021 GLU* 1.3 78.9 - - - +
3041 VAL* 1.3 65.4 + - + +
3061 THR* 3.2 2.4 + - - -
3071 VAL* 3.1 26.8 + - + +
3331 VAL* 4.0 22.0 - - + -
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Residues in contact with VAL 304 (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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2871 ILE* 4.0 13.4 - - + +
2891 VAL* 6.5 0.2 - - + -
3001 ALA 2.9 25.9 + - - +
3011 ARG* 3.7 9.0 - - + +
3031 VAL* 1.3 73.8 - - + +
3051 ALA* 1.3 52.5 + - - +
3071 VAL* 3.2 2.9 + - - +
3081 SER* 2.6 43.5 + - - +
3171 ILE* 4.2 24.5 - - + -
3191 TRP* 3.7 45.5 - - + +
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Residues in contact with ALA 305 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011 ARG* 3.0 17.5 + - + +
3021 GLU* 4.0 4.7 - - - +
3041 VAL* 1.3 75.3 - - - +
3061 THR* 1.3 66.5 + - - +
3081 SER* 3.7 8.0 - - - -
3091 SER* 3.2 24.4 + - - -
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Residues in contact with THR 306 (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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2631 LYS* 5.8 9.1 - - + +
2661 VAL* 4.1 20.5 - - + +
2671 SER* 5.7 3.1 - - - +
2701 LEU* 4.2 11.0 - - + +
3021 GLU* 2.6 32.0 + - - +
3031 VAL* 3.6 4.6 - - - -
3051 ALA* 1.3 76.3 - - - +
3071 VAL* 1.3 58.6 + - - +
3091 SER* 3.0 18.7 + - - -
3101 ARG* 3.6 12.3 - - - +
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Residues in contact with VAL 307 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2661 VAL* 3.7 20.2 - - + -
2701 LEU* 4.4 12.1 - - + -
2851 ALA* 5.2 2.2 - - + -
2871 ILE* 3.8 23.1 - - + -
3031 VAL 3.1 13.9 + - - +
3041 VAL 3.6 5.6 - - - +
3061 THR* 1.3 74.3 - - - +
3081 SER* 1.3 66.6 + - - +
3091 SER 3.1 2.0 - - - -
3101 ARG* 3.0 17.5 + - - +
3111 LEU* 3.6 26.6 + - + +
3351 LEU* 4.0 34.3 - - + -
3371 ILE* 4.9 7.0 - - + -
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Residues in contact with SER 308 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3041 VAL* 2.6 29.6 + - - +
3051 ALA* 3.7 11.7 - - - -
3071 VAL* 1.3 75.9 - - - +
3091 SER* 1.3 59.5 - - - +
3101 ARG 3.6 0.2 + - - -
3111 LEU* 3.8 21.4 + - - +
3121 ASP 4.5 4.3 - - - +
3131 PRO* 5.7 1.4 - - - +
3171 ILE* 3.9 19.8 - - - +
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Residues in contact with SER 309 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3051 ALA 3.2 12.0 + - - -
3061 THR* 3.0 18.5 + - - -
3071 VAL 3.0 0.2 + - - -
3081 SER* 1.3 75.8 - - - +
3101 ARG* 1.3 68.0 + - - +
3111 LEU 3.4 5.2 - - - +
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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